The skin folder is something that should only be in your
source files. !SSL! should show only the names of the outputs you
have generated there. Note that generation and publishing are not
the same thing.
The skin folder should contain a folder for each skin in your
project and they should just contain one .skn file each.
Sounds like it might be time to generate / publish to a new
location to see what you get.
Also, given that this does not sound right, I wonder if it is
behind your other problems with the highlighting issue.
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