tested with gnupg 2.5.20: from time to time, the ownertrust for my own private keys is being dropped, trust reducd from "ultimate"to "unknown".
the issue seems to have appeared after the update to 2.5.20 and wasn't present before. it doesn't affect all private keys at the same time, but strikes for individual private keys in a seemingly random pattern. they work again after restoring ownertrust, until it is being dropped again.
there's no common.conf on the system.
if multiple private keys have lost ownertrust, it is sufficient to claim one key as your own in kleopatra to restore ownertrust also for all other keys.
I can't see any commits pertaining to gpg betweem 2.5.19 and .20 which could cause this. I would say, we need to bisect this but w/o a reliable reproducer this will take too long.
Did you compare ownertrust files exported after the problem occurs with files exported after the problem was "fixed"? A possible explanation would be that the trustdb (re-)calculation aborts in the middle and overwrites the previous correct result with a partial result. (I have no idea how the trustdb (re-)calculation works. Is it "throw everything away and start from scratch"?)