OK, let me lay it out this way, to be more concrete:
Geordi La Forge aboard a
Type VI Shuttle at
Transfer Vaccines
Aboard the shuttle with him are a
Medical Kit and an
Engineering Kit.
Let's say there are no dilemmas under the mission. When Geordi and Shuttle attempt, we know he can solve the mission because we know he has Navigation via his Special Skill and ENGINEER via the EKit and MEDICAL via the MKit.
Sound correct so far?
Now, let's change it up. Let's say Geordi is affected by
Crippling Injury. What skills does Geordi have? How can we find out?
One way is to list off all "regular skills". And if any of those are present, ignore them.
ENGINEER - added via EKit, but it's still a regular, so bye bye.
MEDICAL - added via EKit, but it's still a regular, so bye bye
Navigation - ... ?
Is "Navigation" a "regular skill"? Yes.
Does Geordi have "Navigation"? Arguably, he does, if he can normally solve the mission.
Should it get "lost" due to Crippling Injury? I'd argue yes, because it meets those two criteria.
And if that is the case, how do we
logically give Navigation to Geordi? By "gain" skill mechanism, is my vote.