-> 1. occurs now only if all skills are set correnctly. (nothing has to be changed) -> 2. I don't think that you have to remove all skills from same category. There are just a few: Mantras (Monk), Armors (Wizard: Ice, Storm,...) and Laws (Crus).
update on 1. again: It happens if all skills are set correctly or only passives have to be changed. with my suggestion on 2. here you can speed things up a little bit, even if it's already real quick.
@2: remove all skills only happens if there is alrdy a skill set from that category. to prevent helper from removing skills in those cases set mantra slot and wizard armor slot on the same hotkeyslot. just an example but if doing so d3helper will never start the remove routine