I disagree with several of your points:
1) You misused the pickup skills as markers for pre-placed lemmings. So I don't consider myself responsible to keep such levels functional.
2) Activations of skills has one huge problem: If someone reaches a pickup skill of a non-activated skill, the really should get this skill, but if the level designers disabled the skill, this does not happen.
3) That this problem isn't recognized by the mass replay checked is the real problem here and a bug. Actually when converting levels, this should already be checked.
I am open to suggestions how to solve this, but getting back to manually activating skills is not the way to go.