My game ran perfectly fine up until 2 days ago as I type this. I had a few mods and right before I came here I checked on some websites and those mods were not on any "Do not Download these!" lists that I saw.

So I opened up my game and I discovered to my horror that all of my data had somehow been erased. I thought "fine I'll just start over " after exiting out for the third time. When I opened it back up I found to my growing irritation that it was stuck at 800x600 windowed mode. I have indeed gone in and done the obvious and deselected the windowed mode box, but when I open back up to check to see if the changes have stuck, it reverts back to the 800x600.

I have gone on several other Asks on the web and people said you have to go to SkyrimPrefs.ini, find the Height and Width and change those manually, then save, or else find fullscreen and change the number to = 1. If that doesn't work then you need to do the same thing and save but then make the text file "read only" in order to prevent it from being written over. I've done that and it doesn't change a thing.

It's bad enough that my data is gone, but the fact that it seems hellbent on running in such a small box? It's frustrating as hell. What else could I possibly do to fix this?

Are you editing the right file, it should be located in the %userprofile%\Documents\My Games\Skyrim directory. Your saves should also be located there.

Also....

Are you using Mod organizer? It manages its own ini files, and you must edit them in MO.

I have the same issue also with my resolution being stuck at 800x600 but don't know how to fix it

Try the SKSE plugin "One Tweak"