diff --git a/docs/book/src/cli/watch.md b/docs/book/src/cli/watch.md
index f58f6b7..ddccfd5 100644
--- a/docs/book/src/cli/watch.md
+++ b/docs/book/src/cli/watch.md
@@ -46,9 +46,37 @@ The process responds to `Ctrl+C` and `SIGTERM` for clean shutdown.
 | `--repo <NAME>` | | Repository name for multi-repo indexing |
 | `--source <DIR>` | same as PATH | Source directory to watch (if different from config dir) |
 | `--debounce-ms <MS>` | `500` | Debounce interval in milliseconds |
+| `--reindex-interval-secs <SECS>` | `900` | Periodic full-tree reindex backstop (see below). `0` disables |
 | `--pid-file <FILE>` | | Write PID to this file for daemon management |
 | `--generate-systemd` | | Print a systemd service unit to stdout and exit |
 
+## Reindex backstop
+
+File watchers are the fast path, but they are not a complete freshness
+guarantee: a process restart, a high-churn burst, or a dropped inotify event
+can leave content silently stale until the next manual reindex.
+
+To close that gap, `watch` runs a periodic **reindex backstop** (on by default,
+every 15 minutes). Each sweep reconciles the whole source tree against the
+index — re-embedding any file whose content hash drifted and pruning rows for
+files that have disappeared from disk. Sweeps are incremental: unchanged files
+are skipped by hash, so a sweep where the watcher kept up does almost no work.
+
+Tune the cadence with `--reindex-interval-secs`, or set it to `0` to disable the
+backstop and rely on watcher events alone:
+
+```bash
+# Reconcile every 5 minutes
+bobbin watch --reindex-interval-secs 300
+
+# Disable the backstop
+bobbin watch --reindex-interval-secs 0
+```
+
+`bobbin status` reports a **Freshness** signal — `stale` when the current git
+HEAD is newer than the last index run — so drift is observable without waiting
+for a search to miss.
+
 ## Examples
 
 Watch the current directory:
diff --git a/src/cli/index.rs b/src/cli/index.rs
index 3d9e561..38ea935 100644
--- a/src/cli/index.rs
+++ b/src/cli/index.rs
@@ -1377,7 +1377,7 @@ fn read_indexable_content(path: &Path, config: &Config) -> Result<String> {
 }
 
 /// Collect all files to index based on configuration patterns
-fn collect_files(repo_root: &Path, config: &Config) -> Result<Vec<PathBuf>> {
+pub(crate) fn collect_files(repo_root: &Path, config: &Config) -> Result<Vec<PathBuf>> {
     let mut files = Vec::new();
 
     let mut include_globs: Vec<String> = config.index.include.clone();
diff --git a/src/cli/status.rs b/src/cli/status.rs
index c12d1ee..ebd54ea 100644
--- a/src/cli/status.rs
+++ b/src/cli/status.rs
@@ -40,6 +40,35 @@ struct StatusOutput {
     calibration: Option<CalibrationStatus>,
     #[serde(skip_serializing_if = "Option::is_none")]
     git: Option<GitStatus>,
+    #[serde(skip_serializing_if = "Option::is_none")]
+    freshness: Option<Freshness>,
+}
+
+/// Index freshness relative to git HEAD (bobbin #44).
+#[derive(Serialize)]
+struct Freshness {
+    /// True when HEAD's commit is newer than the last index run (or the repo
+    /// has commits but has never been indexed).
+    stale: bool,
+    /// Committer timestamp (unix seconds) of the current HEAD.
+    head_commit_time: i64,
+    /// Timestamp (unix seconds) of the most recent index run, if any.
+    #[serde(skip_serializing_if = "Option::is_none")]
+    last_indexed: Option<i64>,
+}
+
+impl Freshness {
+    fn compute(head_commit_time: i64, last_indexed: Option<i64>) -> Self {
+        let stale = match last_indexed {
+            Some(ts) => head_commit_time > ts,
+            None => true,
+        };
+        Freshness {
+            stale,
+            head_commit_time,
+            last_indexed,
+        }
+    }
 }
 
 #[derive(Serialize)]
@@ -85,6 +114,7 @@ pub async fn run(args: StatusArgs, output: OutputConfig) -> Result<()> {
                 stats: None,
                 calibration: None,
                 git: None,
+                freshness: None,
             };
             println!("{}", serde_json::to_string_pretty(&json_output)?);
         } else if !output.quiet {
@@ -111,10 +141,16 @@ pub async fn run(args: StatusArgs, output: OutputConfig) -> Result<()> {
     let calibration_result = calibrate::load_calibration(&repo_root);
     let cal_status = build_calibration_status(&calibration_result, stats.total_chunks);
 
-    // Git info
-    let git_status = GitAnalyzer::new(&repo_root)
-        .ok()
-        .map(|git| build_git_status(&git));
+    // Git info + index freshness (bobbin #44): compare HEAD's commit time
+    // against the last index run. If HEAD is newer, committed changes have not
+    // been picked up — a watcher-drift signal that doesn't false-positive on
+    // quiet repos (no new commits => HEAD not newer => not stale).
+    let git = GitAnalyzer::new(&repo_root).ok();
+    let git_status = git.as_ref().map(build_git_status);
+    let freshness = git
+        .as_ref()
+        .and_then(|g| g.get_head_commit_time())
+        .map(|head_ts| Freshness::compute(head_ts, stats.last_indexed));
 
     if output.json {
         let json_output = StatusOutput {
@@ -124,6 +160,7 @@ pub async fn run(args: StatusArgs, output: OutputConfig) -> Result<()> {
             stats: Some(stats),
             calibration: Some(cal_status),
             git: git_status,
+            freshness,
         };
         println!("{}", serde_json::to_string_pretty(&json_output)?);
     } else if !output.quiet {
@@ -168,6 +205,23 @@ pub async fn run(args: StatusArgs, output: OutputConfig) -> Result<()> {
             println!("  Last indexed: {}", dt);
         }
 
+        // Freshness signal (bobbin #44): warn when HEAD outpaces the index.
+        if let Some(ref f) = freshness {
+            if f.stale {
+                let behind = f
+                    .last_indexed
+                    .map(|ts| format!(" (HEAD is {} newer)", format_duration(f.head_commit_time - ts)))
+                    .unwrap_or_else(|| " (never indexed)".to_string());
+                println!(
+                    "  Freshness:    {}{}",
+                    "stale — run `bobbin index`".yellow(),
+                    behind.dimmed()
+                );
+            } else {
+                println!("  Freshness:    {}", "up to date".green());
+            }
+        }
+
         // Show dependency stats
         if let Ok((total_deps, resolved_deps)) = vector_store.get_dependency_stats().await {
             if total_deps > 0 {
@@ -423,6 +477,20 @@ fn format_relative_time(ts: i64) -> String {
     }
 }
 
+/// Format a positive duration in seconds as a compact human string.
+fn format_duration(secs: i64) -> String {
+    let secs = secs.max(0);
+    if secs < 60 {
+        format!("{}s", secs)
+    } else if secs < 3600 {
+        format!("{}m", secs / 60)
+    } else if secs < 86400 {
+        format!("{}h", secs / 3600)
+    } else {
+        format!("{}d", secs / 86400)
+    }
+}
+
 fn format_age_days(days: u32) -> String {
     if days < 30 {
         format!("{} days", days)
@@ -449,6 +517,7 @@ async fn run_remote(args: StatusArgs, output: OutputConfig, server_url: &str) ->
             repos: vec![],
             calibration: None, // Not available via remote
             git: None,         // Not available via remote
+            freshness: None,   // Not available via remote
             stats: Some(IndexStats {
                 total_files: resp.index.total_files,
                 total_chunks: resp.index.total_chunks,
@@ -507,3 +576,47 @@ async fn run_remote(args: StatusArgs, output: OutputConfig, server_url: &str) ->
 
     Ok(())
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_freshness_head_newer_is_stale() {
+        // HEAD committed after the last index run => stale.
+        let f = Freshness::compute(2_000, Some(1_000));
+        assert!(f.stale);
+        assert_eq!(f.head_commit_time, 2_000);
+        assert_eq!(f.last_indexed, Some(1_000));
+    }
+
+    #[test]
+    fn test_freshness_head_older_is_fresh() {
+        // No commits since the last index (quiet repo) => not stale. This is
+        // the false-positive guard: age alone must not flag an idle repo.
+        let f = Freshness::compute(1_000, Some(2_000));
+        assert!(!f.stale);
+    }
+
+    #[test]
+    fn test_freshness_equal_is_fresh() {
+        let f = Freshness::compute(1_000, Some(1_000));
+        assert!(!f.stale);
+    }
+
+    #[test]
+    fn test_freshness_never_indexed_is_stale() {
+        let f = Freshness::compute(1_000, None);
+        assert!(f.stale);
+        assert_eq!(f.last_indexed, None);
+    }
+
+    #[test]
+    fn test_format_duration_units() {
+        assert_eq!(format_duration(30), "30s");
+        assert_eq!(format_duration(120), "2m");
+        assert_eq!(format_duration(7_200), "2h");
+        assert_eq!(format_duration(172_800), "2d");
+        assert_eq!(format_duration(-5), "0s");
+    }
+}
diff --git a/src/cli/watch.rs b/src/cli/watch.rs
index dff9bed..5459e24 100644
--- a/src/cli/watch.rs
+++ b/src/cli/watch.rs
@@ -31,6 +31,13 @@ pub struct WatchArgs {
     #[arg(long, default_value_t = 500)]
     debounce_ms: u64,
 
+    /// Periodic full-tree reindex backstop, in seconds. Catches changes the
+    /// file watcher may have dropped (missed events, high-churn bursts). Each
+    /// sweep is incremental — unchanged files are skipped by hash — so it is
+    /// cheap when the watcher kept up. Set to 0 to disable. (bobbin #44)
+    #[arg(long, default_value_t = 900)]
+    reindex_interval_secs: u64,
+
     /// Write PID to this file for daemon management
     #[arg(long)]
     pid_file: Option<PathBuf>,
@@ -168,6 +175,23 @@ pub async fn run(args: WatchArgs, output: OutputConfig) -> Result<()> {
     let mut compact_counter: usize = 0;
     let mut last_compact = Instant::now();
 
+    // Periodic reindex backstop (bobbin #44). Fires one interval out (not
+    // immediately — the watcher was just started fresh) and reconciles the
+    // whole tree against the index, catching any events the watcher dropped.
+    let reindex_enabled = args.reindex_interval_secs > 0;
+    let reindex_period = Duration::from_secs(args.reindex_interval_secs.max(1));
+    let mut reindex_interval = tokio::time::interval_at(
+        tokio::time::Instant::now() + reindex_period,
+        reindex_period,
+    );
+    reindex_interval.set_missed_tick_behavior(tokio::time::MissedTickBehavior::Skip);
+    if !output.quiet && reindex_enabled {
+        println!(
+            "  Reindex backstop: every {}s",
+            args.reindex_interval_secs
+        );
+    }
+
     let mut sigterm =
         tokio::signal::unix::signal(tokio::signal::unix::SignalKind::terminate())?;
 
@@ -329,6 +353,39 @@ pub async fn run(args: WatchArgs, output: OutputConfig) -> Result<()> {
                     }
                 }
             }
+
+            _ = reindex_interval.tick(), if reindex_enabled => {
+                match run_reindex_backstop(
+                    &source_root,
+                    &config,
+                    repo_name,
+                    &mut vector_store,
+                    &metadata_store,
+                    &embed,
+                    &mut parser,
+                    &output,
+                )
+                .await
+                {
+                    Ok(stats) if stats.files_indexed > 0 || stats.files_removed > 0 => {
+                        compact_counter += stats.files_indexed + stats.files_removed;
+                        if !output.quiet {
+                            println!(
+                                "  {} Backstop reconciled: {} reindexed, {} removed",
+                                "~".cyan(),
+                                stats.files_indexed,
+                                stats.files_removed,
+                            );
+                        }
+                    }
+                    Ok(_) => {}
+                    Err(e) => {
+                        if !output.quiet {
+                            eprintln!("  {} Backstop error: {}", "!".yellow(), e);
+                        }
+                    }
+                }
+            }
         }
     }
 
@@ -482,6 +539,74 @@ async fn reindex_files(
     Ok(stats)
 }
 
+struct BackstopStats {
+    files_indexed: usize,
+    files_removed: usize,
+}
+
+/// Periodic full-tree reconciliation (bobbin #44).
+///
+/// Walks the whole source tree with the same collector `bobbin index` uses,
+/// re-indexes any file whose content hash drifted from the stored one, and
+/// prunes index rows for files that have disappeared from disk. Both halves
+/// reuse the incremental paths (`reindex_files` hash-skips unchanged files),
+/// so a sweep where the watcher kept up does almost no work. This is the
+/// safety net for events the watcher missed (restarts, dropped events,
+/// high-churn bursts).
+#[allow(clippy::too_many_arguments)]
+async fn run_reindex_backstop(
+    source_root: &Path,
+    config: &Config,
+    repo_name: &str,
+    vector_store: &mut VectorStore,
+    metadata_store: &MetadataStore,
+    embed: &Embedder,
+    parser: &mut Parser,
+    output: &OutputConfig,
+) -> Result<BackstopStats> {
+    let files = super::index::collect_files(source_root, config)?;
+
+    // Prune index rows for files that no longer exist on disk. collect_files
+    // only returns extant files, so anything indexed but absent was deleted
+    // while the watcher was down (or its Remove event was dropped).
+    let current: HashSet<String> = files
+        .iter()
+        .map(|p| {
+            p.strip_prefix(source_root)
+                .unwrap_or(p)
+                .to_string_lossy()
+                .to_string()
+        })
+        .collect();
+    let indexed = metadata_store.get_all_indexed_files()?;
+    let removed: Vec<String> = indexed.difference(&current).cloned().collect();
+    let mut files_removed = 0;
+    if !removed.is_empty() {
+        vector_store.delete_by_file(&removed).await?;
+        metadata_store.delete_file_hashes(&removed)?;
+        files_removed = removed.len();
+    }
+
+    // Reindex drifted files (reindex_files skips those whose hash is unchanged).
+    let stats = reindex_files(
+        &files,
+        source_root,
+        config,
+        repo_name,
+        vector_store,
+        metadata_store,
+        embed,
+        parser,
+        output,
+    )
+    .await?;
+
+    Ok(BackstopStats {
+        files_indexed: stats.files_indexed,
+        files_removed,
+    })
+}
+
 /// Detect the git repo name for a directory by walking up to find `.git`.
 /// Returns the directory name containing `.git` (e.g. "moonraker" for
 /// /home/user/workspace/moonraker/src/main.rs).
diff --git a/src/index/git.rs b/src/index/git.rs
index cc12557..ef41b25 100644
--- a/src/index/git.rs
+++ b/src/index/git.rs
@@ -332,6 +332,23 @@ impl GitAnalyzer {
         Ok(String::from_utf8_lossy(&output.stdout).trim().to_string())
     }
 
+    /// Get the committer timestamp (unix seconds) of the current HEAD commit.
+    ///
+    /// Used as a freshness reference: if HEAD is newer than the last index run,
+    /// committed changes have not yet been picked up (bobbin #44). Returns None
+    /// when there is no HEAD (empty repo) or git is unavailable.
+    pub fn get_head_commit_time(&self) -> Option<i64> {
+        let output = Command::new("git")
+            .args(["log", "-1", "--format=%ct"])
+            .current_dir(&self.repo_root)
+            .output()
+            .ok()?;
+        if !output.status.success() {
+            return None;
+        }
+        String::from_utf8_lossy(&output.stdout).trim().parse::<i64>().ok()
+    }
+
     /// Get the last commit timestamp for every file in the repo in one pass.
     ///
     /// Returns a map of relative file path -> unix timestamp of the most recent