Regarding the stock game corruption when deactivating FOTRSU_v0.40 Beta, I've taken a look at the mods file in question...the NPL_Conte_Verde. Stock game has 18 total files while FORTSU has around 64. I know why (having additional skins for the ship), but there are files that shouldn't be in there.
I've highlighted a file named "Euroliner.zon-remove" that has 0 KB for its size (meaning its a dummy file):
Just below it is another file similar in name "EuroLiner.zon" with a file size of 30 KB. So, this .zon file has something in it, but it's also one of 5 Stock game files that becomes misplaced when you remove the mod from activation. May I suggest whoever put this file together to fix it.
Also, the reason the Netherlands Search Plane doesn't have a skin is simply due to not having a skin where one should have been. Below, in the smaller window is the Netherlands Search Plane .cfg file from the Roster folder that points to a texture named "ALBS_PBYCatalina_T02.tga":
The larger image shows the mods contents of the ALBS_PBYCatalina folder, with
no T02 texture image. No skin for you!!