[Bug]: Live records become unreachable by query() after deletes and upserts while get() still returns them (1.5.9)

"""Standalone reproduction for the disclosure: live records unreachable by search
in Chroma after heavy deletes/upserts. No vfo dependency. ~1 minute.

    pip install chromadb numpy && python repro_chroma_unreachable.py [seed]

Builds the collection, lists live records that a query with their own stored vector
does not return (top-100 and top-1,000), then reopens the store in a fresh Python
process and checks again. The affected records differ between runs even with the
same seed (index construction is not deterministic), so run it a few times.
"""
import subprocess, sys, tempfile
import chromadb, numpy as np


def unreachable(col, k_top):
    g = col.get(include=["embeddings"])
    out = []
    for i, e in zip(g["ids"], g["embeddings"]):
        r = col.query(query_embeddings=[list(e)], n_results=k_top)
        if i not in r["ids"][0]:
            out.append(int(i))
    return len(g["ids"]), sorted(out)


def check(path, label):
    col = chromadb.PersistentClient(path=path).get_collection("repro")
    n_live, miss100 = unreachable(col, 100)
    _, miss1000 = unreachable(col, 1000)
    print(f"{label}: {n_live} live records; not returned for their own vector: "
          f"top-100 {len(miss100)} {miss100}, top-1000 {len(miss1000)} {miss1000}", flush=True)
    for k in miss1000:
        g = col.get(ids=[str(k)], include=["embeddings"])
        print(f"  id {k}: get() found={bool(g['ids'])}", flush=True)


if len(sys.argv) > 2 and sys.argv[1] == "--check":
    check(sys.argv[2], "after reopen in a new process")
    sys.exit(0)

seed = int(sys.argv[1]) if len(sys.argv) > 1 else 3
rng = np.random.default_rng(seed)
path = tempfile.mkdtemp()
col = chromadb.PersistentClient(path=path).get_or_create_collection("repro", metadata={"hnsw:space": "l2"})
n, d = 4000, 32
X = rng.standard_normal((n, d)).astype(np.float32)
for i in range(0, n, 500):
    col.add(ids=[str(j) for j in range(i, i + 500)], embeddings=X[i:i + 500].tolist())
live = set(range(n))
dele = rng.choice(n, n // 2, replace=False)
col.delete(ids=[str(int(k)) for k in dele]); live -= set(dele.tolist())
up = rng.choice(sorted(live), int(0.3 * len(live)), replace=False)
col.upsert(ids=[str(int(k)) for k in up], embeddings=rng.standard_normal((len(up), d)).astype(np.float32).tolist())

print(f"chromadb {chromadb.__version__}, seed {seed}", flush=True)
check(path, "same process")
subprocess.run([sys.executable, __file__, "--check", path], check=True)