This has been a problem for a long time, but we have now added safeguards and a repair function.
The safeguards checks for the problem at strategic times, so we can hone in on when it possibly happens. The repair function can clean up the database so it is working again.
These fixes are available in canary 2.1.0.116.
The easy way is to install the canary build, and use the repair method there.
However, since you are on 2.0.8.1, this requires a database upgrade (from 2.1.0.5 stable and forward). The database upgrade is automatic, but downgrade is a manual process.
If you prefer not to do that, then one solution is to use the commandline (either actual commandline, or the commandline emulator from the UI) and delete the defect versions.
Another could be to attempt to recreate the database.
Let me know if you need advice on one of the suggested ways.