Thanks for sticking with me. I did have copies of most of the other files, but that db file was where most of the useful data was, and as said, no history there.
Having a way to restore some of the files after they have been destroyed by a glaring Github integration bug is not really a solution, so unfortunately I really cannot mark this issue as resolved.
I have also sent a message via the support form.
(In case there is nothing that support can do about this either, I am planning my replit exit strategy, as something like this issue, combined with the latest move of nerfing the Hacker plans in the middle of a paid subscription period, has not put me in a very positive mood.)