Was changing trinkets around for a fight and after fight I went to my exploration set up and noticed my horseshoe jump trinket was no longer showing.
Checked and it doesnt even say I own it anymore.

No idea how or why it happened just randomly did.

was playing a modded Mineshaft & monsters 1.16.5 server

Having the same issue occur, just lost two trinkets this way. Playing FTB Endeavor with no configurations to default.

I have been having this issue repeatedly in my game. I am playing Enigmatica 6 Expert, on MC 1.16.5. When I remove a trinket and replace it, I sometimes lose the trinket and it is not there any more when I go to pick it again. This only started happening after I reached the "maximum" of 3 rows of trinkets discovered. I thin, but can't be sure, that it may happen if I clear a trinket and don't select another one before closing the trinket GUI, thus having "too many" and it deletes one at random. I have tracked which ones dissappear, loosely, and it is not the oldest or least used ones, or any other pattern I can see. I have lost all class levels from common to legendary (ouch that one hurt, I used it all the time in battles).
Perhaps we don't need a limit on how many are discovered? Or you could make a way to select which ones we don't want any more, and they get lost, and have a low chance of being rediscovered?