I have been using endnote forever too. I have only once had this problem (and luckily had backups and synced copies). In my case I intermittently lost access to our network drive. At that time, I was told only use the library on local haddrive. I have to be honest, I didn’t like or heed that advice and haven’t had the trouble again. But it is worth looking at where your library lives and thinking about trialing it on the hard drive for a bit?
I assume when you moved/renamed things, you did take the .DATA folder too? That is where the guts of the database reside.