Can't say but I am pretty sure it won't remove them since the installer doesn't purge the entire Skyrim folder. If you are worried about stuff you can always make a copy of your folders before uninstall. One is in Documents/Mygames/Skyrim and the other is in ProgramFiles(x86)/Steam/Steamapps/Common/Skyrim. Your mod files should be in the latter.
Good point about copy of install.. I still have a backup of 11/11/11 Day of release ...installed Skyrim...took me about 2 Hours to figure out that I was going to have problems with Steam / Skyrim / WryeBash &MODs until I moved steam OUT of "Program Files". So did a Steam Move...and have the Back-up I created for the move....
And, one more directory Skyrim likes to play in it seems......{your user name]\AppData\Local\SkyrimI have 3 files in there, have read that these files are now used by the launcher to control load order. One, or more of these files could be because I use Wrye Bash. I would think that leaving any files in here (pertaining to load order) could confuse Skyrim and the launcher after a wipe of the install. They (bethesda ) changed the rules, and I am still learning the rules...lol
Worst thing about it is ....This is a hidden directory.....in order to see it you have to have..."show hidden files" set in your folder options. This svcks because now you will have garbage on your desktop (desktop INI), and extra directories (Virtual links ).
Rules....learn them or sink...
