I was having issues like this a couple years ago, not much with audio but with bank files being corrupted and also even more strangely sometimes I would save a project and reopen it and it wouldn’t give me an error but some of the parameters would be changed in really weird ways (record parameters for track 1 moving to track 5 was a common one, as was the record source being changed from whatever it had been before saving and reloading to SRC3 - Track 7, once or twice track trigs would move from one pattern to another and IIRC I had one instance where a track that had been center panned ended up hard panned to one side; once this happened to a project it would persist - it was an actual problem with the files on the card).
It started after I had to make a two hour drive with the OT in the drunk of a car during the worst cold snap in a decade, and what ended up fixing it was doing a low level reformat of the CF card on a computer with a dedicated CF formatting program. Reformatting on the OT didn’t work and reformatting with the OSes own reformat function didn’t work. I honestly can’ remember what program I used, I tried a few and only one of them would complete the format (which took about 20 minutes) without locking up near the end. Been using the same card since then and it never happened again after the reformat, as far as I can figure the project files were being corrupted but the OT was still able to read them, it was just reading incorrect values for some things.
This is the post where I described what I did in more detail, maybe it will help you.
EDIT: also, ever since that drive encoder A has been jsut a bit jittery if I run it slow (but responds like normal when I turn it fast) - not bad enough to replace it but enough that I notice it compared to how it was before and how all the other encoders still are. The moral here is don’t let your OT get too cold!