I found a bug that triggers when you kill joneleth and go to hell.
If you use project image / simulacrum in that battle, and have them use your spell sequencer or minor spell sequencer, when joneleth is killed and you are drawn to hell, either sequencer that your image has used will no longer be available to your character permanently!
This sequencer is not just gone, but you can never recast that sequencer, because you still have it 'prepared', but not available on your special abilities hotkey anymore, so any attempt to recast it just results in the message that you already have one, and you can't have 2, even though it is not available to be used on your hotkey. (you can't cancel sequencers like you can with contingencies).
I had this happen to me for both imoen and aerie, arie's image or simulcrum had used a minor sequencer, and imoen's had used both minor and regular sequencer, which were permanently unavailable after that (just the minor was bugged for aerie, but both were lost to imoen).
I did not notice it until a bit into throne of baal (it continues to be bugged).
When checking old saves, I found where it occured, and I replayed killing joneleth without using any seqencers, and I didn't lose them in that case, but I didn't keep this replay, since I came to far into tob to go back at that point.
Using image / simulcrum to then use your sequencers is a very powerful and repeatable trick which I used for the bosses, and once permanently unavailable, it's a big loss.