Quote:
Originally Posted by Illyahr
When a template replaces bonus feats, it moves one bonus feat farther down instead of replacing it. For example, a level 8 fighter with resolve, aligned strike, and elusive attack (replacing the feats at 2,4, and 6) still has 3 bonus feats (should have 2, one for level 1 and one for level 8) and the overview shows two bonus feats at level 8.
Variants that replace a thing that has a bootstrap don't turn off the bootstrap (example, replacing the rogue's trapfinding only replaces the class ability and not the bootstrapped ability)
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Can you be more specific about which templates and class variants? Unfortunately, there isn't a way to affect all templates/variants to fix issues like this. It will have to be done on a case-by-case basis.