Came across a possible character import bug. I just tried to import my previous level 40 character into a new ToB game and noticed that most of his HLAs, namely the ones from this mod, were missing. I closed down the game and opened up the character in Shadowkeeper and, sure enough, all my abilities were present and counted for. I tried importing the character again and the HLAs were still gone.
Sounds like an engine issue.
If that is the case, there's probably very little we can do about it.