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I'm not sure about the exact nature of this problem but first thing to try would be to re-extract RttUNNv1.01_sky+spawn-patched.7z into the main folder. Also I'd highly recommend to use the mod manager.
EDIT: Way to sneak in through the backdoor G'len. Welcome back.
The thing is that I intend to use ShockEd, which is incompatible with it.
renaiming LGVID.AX did the magic :p
The current folder being write protected is normal. The problem is unlikely to be due to this FM.The overwriting of quicksaves during level loading is in fact the game's default behaviour.Quicksaves only become permanent with the SS2Tool's "Keybind Fix" or making the according changes manually. Loading one of the predefined keysets in the game, will change this back again.Now this is still unlikely to keep you from entering other decks. A faulty game setup is more probable. SS2 Tech FAQ
Whichever way the quicksave got corrupted....here's how to fix permanent quicksaves.