Delete not Persisted

**Question**
I am trying to delete a record using box.delete but every time I reload, everything comes back.
Checking the data, it is deleted in memory, but the changes are not persisted.

**Code sample**
```
var box = await Hive.openBox(hiveBox);
await box.delete(nodeID);
await box.compact();
```

**Version**
- Platform: Mac, Windows
- Flutter version: Channel stable, 3.7.11,
- Hive version: ^2.2.3

Start with the box.delete and box.compact entry points shown in the report, then reproduce the behavior by deleting a key, compacting the box, and reopening it. Trace the persistence path to determine why the deletion is present in memory but absent after reload; done means the deleted record remains absent on Mac and Windows with the reported versions.

Written by the indexing model from the issue text.