Hmm alright can you reach out directly to support@figma.com. We’ll ideally need to take a look at the files to see why this might still be happening.
If you can reach out and share both the library file and instances file with us, with edit access (please give edit access to support-share@figma.com)
Also if you could point us to the exact instance that’s experiencing the problem and the exact overrides that are lost, that would be super helpful.
Thanks