Whenever you swap out a feat, it takes in account the LEVEL you are swapping out at and what tomes apply at that level. Dillante is a level ONE feat. There are no tomes that apply at level one. So when you swap out a level one feat when you are level 20, it is still using the stats you had at level one (base created stats) and does not take into account tomes that only apply at later levels.
Having a similar problem.
Just capped to 20 and wanted to swap out cleric diletante for rogue. (yes I have the pre-req stats at level 1 before any tomes added).
Cleric dilletante is not even showing in the feat list to be able to swap it for anything. Wish i'd known this was broken before I leveled the character but alas Devs don't think its worth adding to the known issues list. Guess selling extra LR hearts of wood makes a good argument for not listing it. ;-p