diff --git a/src/capnp_store.rs b/src/capnp_store.rs
index d48cb5a..d32716f 100644
--- a/src/capnp_store.rs
+++ b/src/capnp_store.rs
@@ -356,6 +356,7 @@ impl StoreView for Store {
 
     fn for_each_relation<F: FnMut(&str, &str, f32, RelationType)>(&self, mut f: F) {
         for rel in &self.relations {
+            if rel.deleted { continue; }
             f(&rel.source_key, &rel.target_key, rel.strength, rel.rel_type);
         }
     }
@@ -431,6 +432,7 @@ impl StoreView for MmapView {
     fn for_each_relation<F: FnMut(&str, &str, f32, RelationType)>(&self, mut f: F) {
         let snap = self.snapshot();
         for rel in snap.relations.iter() {
+            if rel.deleted { continue; }
             let rt = match rel.rel_type {
                 ArchivedRelationType::Link => RelationType::Link,
                 ArchivedRelationType::Causal => RelationType::Causal,
@@ -752,7 +754,7 @@ impl Store {
     fn save_snapshot_inner(&self) -> Result<(), String> {
         let snap = Snapshot {
             nodes: self.nodes.clone(),
-            relations: self.relations.clone(),
+            relations: self.relations.iter().filter(|r| !r.deleted).cloned().collect(),
             gaps: self.gaps.clone(),
             params: self.params.clone(),
         };
@@ -1485,6 +1487,9 @@ impl Store {
             self.append_relations(&pruned_rels)?;
         }
 
+        // Remove deleted relations from in-memory vec so save() is clean
+        self.relations.retain(|r| !r.deleted);
+
         Ok((hubs_capped, to_delete.len()))
     }