you are out of luck
the windows restore function will only "remove" things that were recently added but it cant put back things that were deleted so it cant really "restore" as it is named but it is really just a very powerfull uninstaller feature
you are going to need to delete the remaining folders with the leftovers from any mods you had installed or it will corrupt the new game install. your saved games will need the game set up exactly as it was with the mods and all or they will CTD so most likely consider them fubar as well unless you are very lucky to remember everything about how it was set up
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