Yes but won't that overwrite my skyrim.ini and any of the scripts I've edited for mods I'm making? I guess I could backup my whole folder to be safe.
Make a backup of the scripts for your mods, and make a backup of your ini file, or any modded file that has replaced a stock file, because it could restore that back to default. i own gmod and have so many mods installed for it, verifying the integrity of game cache doesn't remove added files, it will replace corrupt and missing game files you get with the game, and that can include official scripts that came with the game that have been altered. Added files for Mods are left untouched from what i have seen.
I have ran this on every game i have bought on steam, many of those games have added mods installed, none of those mods replace stock files that i know of, and those mods are still working fine. It normally only messes around with official game files that come with the game.