Well there's a bug atm with holy pomanders apperantly. If you take a subclass get 3rd class you get the holy pomanders, however if you decide to delete that sub and later on decide to make it again, you won't get holy pomanders anymore (and neither skills, ofcourse).
Since these items can only be in inventory (not depositable etc) then I belive best solution would be to unset the variable related to holy pomander when deleting a subclass incase a pomander cannot be found in inventory (Which means in other words that it was used for learning a skill, which will get erased anyway upon sub deletion).
Confirmed.