Bug Report: DROP_VECTOR_INDEX leaves corrupted metadata preventing property updates

Environment

• Kuzu Version: 0.11.2
• Storage Version: 39
• API: REST API (kuzudb/api-server:latest)
• Vector Extension: Loaded via LOAD EXTENSION VECTOR

Summary

After creating and dropping a vector index on a property, that property becomes permanently un-updatable via SET or MERGE operations. The error persists even after:

• Dropping the vector index (confirmed via SHOW_INDEXES())
• Restarting the database
• No indexes remaining in the catalog

Expected Behavior

After DROP_VECTOR_INDEX successfully removes a vector index, the property should be updatable again via SET or MERGE operations.

Actual Behavior

The property remains permanently un-updatable with error:

Runtime exception: Cannot set property vec in table embeddings because it is used in one or more indexes. Try delete and then insert.

Note: No table named "embeddings" exists in the catalog, suggesting this is an internal metadata structure.

Impact

This bug makes vector indexes incompatible with mutable data:

• Cannot update entity properties that have embeddings
• Breaks MERGE-based upsert workflows
• Makes incremental data updates impractical

Root Cause Analysis

After deeper investigation into the source code, I suspect the bug is in NodeTable::dropIndex():

File: src/storage/store/node_table.cpp

void NodeTable::addIndex(std::unique_ptr<Index> index) {
    // ...
    indexes.push_back(IndexHolder{std::move(index)});
    hasChanges = true;  // ← Marks table for checkpoint
}

void NodeTable::dropIndex(const std::string& name) {
    KU_ASSERT(getIndex(name) != nullptr);
    for (auto it = indexes.begin(); it != indexes.end(); ++it) {
        if (StringUtils::caseInsensitiveEquals(it->getName(), name)) {
            KU_ASSERT(it->isLoaded());
            indexes.erase(it);
            return;  // ← BUG: Missing hasChanges = true!
        }
    }
}

What happens:

1. DROP_VECTOR_INDEX calls Catalog::dropIndex() → removes from catalog ✓
2. DROP_VECTOR_INDEX calls NodeTable::dropIndex() → removes from in-memory indexes vector ✓
3. BUT NodeTable::dropIndex() doesn't set hasChanges = true
4. On checkpoint, the table's serialization includes the OLD indexes (from disk)
5. On restart/reload, NodeTable::deserialize() loads the persisted indexes vector which still contains the dropped index

File: src/storage/store/node_table.cpp

void NodeTable::serialize(Serializer& serializer) const {
    nodeGroups->serialize(serializer);
    serializer.write<uint64_t>(indexes.size());  // ← Serializes indexes vector
    for (auto i = 0u; i < indexes.size(); ++i) {
        indexes[i].serialize(serializer);
    }
}

void NodeTable::deserialize(...) {
    // ...
    indexes.clear();
    indexes.reserve(indexInfos.size());
    for (auto i = 0u; i < indexInfos.size(); ++i) {
        indexes.push_back(IndexHolder(...));  // ← Reloads old indexes from disk
    }
}

Why updates fail:

When updating a property, NodeTable::initUpdateState() iterates through the indexes vector and calls each index's initUpdateState():

void NodeTable::initUpdateState(...) {
    for (auto i = 0u; i < indexes.size(); i++) {
        auto& indexHolder = indexes[i];
        auto index = indexHolder.getIndex();
        if (index->isBuiltOnColumn(nodeUpdateState.columnID)) {
            // Calls HNSWIndex::initUpdateState() which throws error
            nodeUpdateState.indexUpdateState[i] = index->initUpdateState(...);
        }
    }
}

The HNSW index's initUpdateState() is hardcoded to throw:

File: extension/vector/src/include/index/hnsw_index.h

std::unique_ptr<UpdateState> initUpdateState(...) override {
    throw common::RuntimeException{
        "Cannot set property vec in table embeddings because it is "
        "used in one or more indexes. Try delete and then insert."
    };
}

The Fix

Add hasChanges = true in NodeTable::dropIndex():

void NodeTable::dropIndex(const std::string& name) {
    KU_ASSERT(getIndex(name) != nullptr);
    for (auto it = indexes.begin(); it != indexes.end(); ++it) {
        if (StringUtils::caseInsensitiveEquals(it->getName(), name)) {
            KU_ASSERT(it->isLoaded());
            indexes.erase(it);
            hasChanges = true;  // ← Add this line
            return;
        }
    }
}

This ensures the NodeTable gets checkpointed with the updated indexes vector, and on restart/reload, the dropped index won't be in the collection.

Are there known steps to reproduce?

Minimal Reproducible Example

-- Step 1: Create a node table with vector property
CREATE NODE TABLE Person(id STRING, name STRING, embeddings FLOAT[128], PRIMARY KEY(id));

-- Step 2: Insert a test node
CREATE (p:Person {id: "person-1", name: "Alice", embeddings: [0.1, 0.2, 0.3, ..., 0.128]});

-- Step 3: Create vector index on embeddings property
CALL CREATE_VECTOR_INDEX(
    'Person',
    'person_embeddings_idx',
    'embeddings',
    mu := 30,
    ml := 60,
    pu := 0.05,
    metric := 'cosine',
    efc := 200,
    cache_embeddings := true
);

-- Step 4: Verify index was created
CALL SHOW_INDEXES() RETURN *;
-- Output: Shows person_embeddings_idx on Person.embeddings

-- Step 5: Drop the vector index
CALL DROP_VECTOR_INDEX('Person', 'person_embeddings_idx');
-- Output: "Table _X_person_embeddings_idx_LOWER has been dropped."

-- Step 6: Verify index was removed
CALL SHOW_INDEXES() RETURN *;
-- Output: Empty result (no indexes remain)

-- Step 7: Try to update the embeddings property
MATCH (p:Person {id: "person-1"})
SET p.embeddings = [0.2, 0.3, 0.4, ..., 0.129]
RETURN p.id;

-- ERROR: Runtime exception: Cannot set property vec in table embeddings because it is used in one or more indexes. Try delete and then insert.

Additional Observations

The problem is table-specific

-- Create another table that never had a vector index
CREATE NODE TABLE Organization(id STRING, name STRING, embeddings FLOAT[128], PRIMARY KEY(id));
CREATE (o:Organization {id: "org-1", name: "Company", embeddings: [0.1, 0.2, ...]});

-- This works fine (no index was ever created)
MATCH (o:Organization {id: "org-1"})
SET o.embeddings = [0.2, 0.3, ...]
RETURN o.id;
-- Success!

-- But Person table (which had an index) remains broken
MATCH (p:Person {id: "person-1"})
SET p.embeddings = [0.2, 0.3, ...]
RETURN p.id;
-- Still fails with same error

Other properties are unaffected

-- Non-indexed properties on the same table work fine
MATCH (p:Person {id: "person-1"})
SET p.name = "Updated Name"
RETURN p.name;
-- Success!

The issue persists across database restarts

After restarting the Kuzu server, the same error occurs, indicating the corrupted metadata is persisted to disk.