diff --git a/src/cli/admin.rs b/src/cli/admin.rs
index de3c987..a9cca43 100644
--- a/src/cli/admin.rs
+++ b/src/cli/admin.rs
@@ -61,7 +61,7 @@ pub async fn cmd_fsck() -> Result<()> {
     store::fsck()?;
 
     let arc = memory::access_local()?;
-    let mut store = arc.lock().await;
+    let store = arc.lock().await;
 
     // Check node-key consistency
     let mut issues = 0;
@@ -287,8 +287,9 @@ pub async fn cmd_dedup(apply: bool) -> Result<()> {
         merged += doomed_uuids.len();
     }
 
-    // Remove tombstoned relations from cache
+    // Remove tombstoned relations from cache and rebuild index
     store.relations.retain(|r| !r.deleted);
+    store.reindex_relations()?;
     store.save()?;
 
     println!("Merged {} duplicates, redirected {} edges, deduped {} duplicate edges",
diff --git a/src/hippocampus/store/index.rs b/src/hippocampus/store/index.rs
index 43bbb4f..6615f72 100644
--- a/src/hippocampus/store/index.rs
+++ b/src/hippocampus/store/index.rs
@@ -209,6 +209,18 @@ pub fn remove_relation(
     Ok(())
 }
 
+/// Clear all relations from the index.
+pub fn clear_relations(db: &Database) -> Result<()> {
+    let txn = db.begin_write()?;
+    {
+        // Drop and recreate the table
+        txn.delete_multimap_table(RELS)?;
+        let _ = txn.open_multimap_table(RELS)?;
+    }
+    txn.commit()?;
+    Ok(())
+}
+
 /// Get all edges for a node. Returns (other_uuid, strength, rel_type, is_outgoing).
 pub fn edges_for_node(db: &Database, node_uuid: &[u8; 16]) -> Result<Vec<([u8; 16], f32, u8, bool)>> {
     let txn = db.begin_read()?;
diff --git a/src/hippocampus/store/mod.rs b/src/hippocampus/store/mod.rs
index c9d57e5..eef031a 100644
--- a/src/hippocampus/store/mod.rs
+++ b/src/hippocampus/store/mod.rs
@@ -130,6 +130,18 @@ impl Store {
         Ok(())
     }
 
+    /// Rebuild relation index from Vec. Call after mutations that modify relations.
+    pub fn reindex_relations(&self) -> Result<()> {
+        if let Some(db) = self.db.as_ref() {
+            index::clear_relations(db)?;
+            for rel in &self.relations {
+                if rel.deleted { continue; }
+                index::index_relation(db, &rel.source, &rel.target, rel.strength, rel.rel_type as u8)?;
+            }
+        }
+        Ok(())
+    }
+
     pub fn resolve_key(&self, target: &str) -> Result<String> {
         // Strip .md suffix if present — keys no longer use it
         let bare = strip_md_suffix(target);