Elite skills: keep the disabled skill elite, so that I could return to it later. Otherwise I'm pretty much locked out of elite promotions for skills I'm not 100% certain I'll never re-roll.
Permanent skills: allow to reassign, with following drawbacks:
- Officer Management: pop extra officers above cap from ships and prevent reassignment (same as when you pick up extra officers from pods)
- Officer Training: officer max and current level reduced to 5, officers with 6 skills get popped from ships and can't be reassigned until you pick 1 skill to remove.
- Special Modifications: any ship with above current cap vents/caps or 3 built-in hullmods suffer massive max CR reduction and/or high malfunction rate at any CR. This one I'm less certain about, since there doesn't seem to be as clean way to undo it. One option is to allow to remove built-in hullmods (optionally refunding spent SP cost: for example if it granted 70% bonus exp when built-in, the committed cost to be refunded is 30%).