I always keep a copy of my ini files (in your My Games folder), just in case verifying the cache replaces them for whatever reason. I'd recommend doing that as well prior to the verification.
^ ^ This...good advice for anyone. Every 2 days or do, if the game is running smoothly, I create a copy of those ini file in a backup folder (as well as my injector files). I also read-only my main two ini files, and hand-tune any setting changes I want, cause I just don't trust this game's architecture yet. The launcher is buggy and seems to randomly think my settings need checking. And with the stealth Steam updates, I don't want my settings nuked. After I see a patch has been installed, I move my current ini's to backup, then do a "check local integrity" check for Skyrim in Steam. It now creates new ini's...so now I do a "compare" using Notepad++ between 'new' and 'old' inis, just to see if Bethesda has added anything shiny and new that will magically fix stutters, improve the interface to something PC users may appreciate, or whatever (dare to dream).
Seems extreme, but now the Bethesda/Steam kabal can't do anything I can't undo.