Mail Removed the Flags from all Flagged Emails - can they be recovered?

I stupidly decided to try Tahoe again once the first patches were out. I have - for decades - used flags in Mail to sort important emails in to different categories. The first thing I noticed about Tahoe Mail was that new emails would come in with some flags already displayed, as if Mail has decided that it knows better than me which emails shoudl be flagged in which colors (spoiler - it does not). I have not found a way to address this, but now it is moot: all flags are effectively gone. I say "effectively gone" because if I find the email I am looking for, it DISPLAYS with the flag I chose. But in the sidebar, the "Flagged" section shows zero flagged emails, as does searching for "flagged" in the search bar.

Has anyone else found this issue and - more importantly - have you found a fix? This is ALL my email organization corrupted.