Is there a difference between updating iOS via OTA or iTunes? I have done some pretty good mucking around with my iPhone 4S's filesystem (e.g. deleting my Music folder). I have an inkling that the iTunes update is more thorough, and will reformat my entire filesystem, while I'm not so sure about the OTA update.
Does anyone have any in-depth knowledge they'd like to share on the matter?
Edit: I'll be going from 5.0.1 to 5.1.1