It is possible to give the main character a "duplicate" of the skill, which will take effect. (cf. this thread with console commands: http://forums.obsidian.net/topic/71903-console-commandscheats/page-3) I do not know, however, if you can remove the duplicate skill in case the much anticipated fix is retroactive... wouldn't want my character to wind up with two "Towering Physique", "Armored Grace", and "Confident Aim" buffs permanently active.
If I use the AddAbility command to re-enable the abilities my character lost to the double-click inventory bug, can I remove the ineffective duplicates? Would be especially relevant if the hotfix is retroactive.