I don't recall running into this specifically, but my first suggestion would have been to run Drive Check, which you apparently have done already.

Do you still have the ability to Redo that one level of Undo?
If so, then I might suggest redoing it and firstly see if the track will consistently play back the way it should.

If it does, then I would suggest doing a track bounce of just that comp'd track to an unused channel in order to acquire a contiguous recording of the complete performance of that track. I would do this regardless of whether or not you can recover that one level of undo.

If you bounce the track and it contains some error you tried to eliminate with that one undo procedure, than at least you can later use that contiguous track to perform the correction/punch-in you need and probably not experience the same issue again.

If you can bounce the track without redoing that one level of undo and get it to record the bounce without scrambling anything for a full pass of the track, then that's really the ideal scenario - it might take more than one attempt at the bounce to get it done, or maybe you could perform the bounce in short passes, completing the track in chunks, just for the sake of having a new version of the comp'd track and avoid the playback issues you're no experiencing.

Once you get a complete bounce of the comp'd track, then I'd suggest either shelving the original comp to an unused virtual layer, or deleting it completely. Then at the first opportunity (without the risk of losing important potential undo levels), I would perform a Song Optimize on the project before you go much farther.

I would also take the opportunity to back up every important project to whatever media you usually do this to and then reinitialize your hard drive (that means every partition must be backed up before you reinitialize, since that will wipe the entire hard drive clean).

If Drive Check didn't find errors, then the hard drive itself must have issues - maybe reinitializing it will solve those issues. It's also possible that your hard drive may be showing signs of failure, if it is many years old.
When you reinitialize, don't turn on physical format, but maybe check the scan option.... I don't remember the whole initialize screen anymore, so sorry if I'm mis-stating things here. Hopefully you understand what I am suggesting.