[SOLVED] WHAT THE DUCK?
Why don't you try to narrow down the possibilities rather than doing nothing and hoping for someone's random speculation to be correct? None of us can debug this for you based on your vague account of what you edited and trusting that you didn't screw something up. As we all know, Hammer is extremely user friendly for new users, and it's nearly impossible to make a mistake.
Back up your instances folder, then verify game cache. If it works then we know instance edits are the problem. If it doesn't then we have ruled out instances as causing the problem. Either way, we have gained useful information and are closer to finding out what's wrong. And you won't lose your edits.
Portal 1: Portal Pro, Resurrection, Dyad, Rexaura
Portal 2: [Coop] Electrophobia, [PTI] EotM Collection, [SP] Aperture Halloween
Mevious is smarter than you. Do what he says or shut up. And it's your own damn fault that you've edited stock instances.
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I was hoping to find out this was a problem that wasn't only effecting me, or that it was a problem that had come up before and had a simple fix like "Yep. You need to make a logic_auto with onmapspawn blah blah blah". I guess if I back up my entire instance folder, validate, and then delete the new one and replace it with the old it will fix it. I really have no clue how the hell this could of happened, since it seems to of happened over night....
one thing, if I just re locate my instance folder (somewhere out of the steam files, probably programfiles (x86)), will Steam still hunt it down and "fix" it when I validate the cache?
There is a simple fix, it's verifying your game cache. And yes, moving files to another location is what we in the industry call "backing up".
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Generally backing up files means putting it on something other than the computer's hard drive.... I guess it doesn't matter, it doesn't delete anything in the map folder so I'm just copying all the vmfs to the map folder.
Well... great, validated after backing up files... then I replaced the folders, first I tried to replace just p2editor, but that failed (somehow everything had a duplicate of itself, but it was a vmx file?) and nothing compiled. Then I went and got the instance file I hid away in program files (x86), copied it to sdk_content -> maps, and all it had in it was Felix griffin's animal king (and smashable glass)!? I didn't even have those installed, I just had them sitting on my comp because they're broken right now (won't work in the pti like they're supposed to). So, ruined instances, need to re validate, and spend another 3 hours re doing my instances.
RE-RE VALIDATE AND NOW MY INSTANCE FOLDER ONLY HAS P2EDITOR.
Check it before re-adding in your edited instances. If it compiles you know one of your changes is at fault.
vmxs are copies of vmfs, they are back ups
and you are a moron if you couldn't back up properly
what happened to your avatar I was going to use that in a map 
and you are a moron if you couldn't back up properly
what happened to your avatar I was going to use that in a map
Msleeper decided she didn't like it. Lol good idea, though.
It wasn't my instances, I re did everything and the entrance room loaded. Everything is exactly the way it was (well, my lights are a different color.. but that wouldn't change anything) when it stopped working.
And ben, I did back it up correctly... I have no clue how the hell FG's animal king got in my instances, nor how copying the entire instance folder would only copy FG's animal king.
So, validating the Authoring Tools didn't help? Um, what was that Weatherbug thing I recall seeing?
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[spoiler]Maps:
Revenge of the Angry Turrets
Capture the Cube [Co-op]
Capture the Cube 2 [Co-op]
TPWEGTH Sample Map
Aperture Aquatic Testing Center
Aperture Aquatic Testing Center 2
Aperture Time Testing Center
ML's Halloween Trick - 1000 downloads!
ML's Halloween Treat
ML's Combination - 1000 downloads!
ML's Jailbreak Labyrinth
ML's Tricky Teamwork [Co-op]
WIP:
"Capture the Cube 3"
Workshop Maps Link: http://steamcommunity.com/profiles/76561198008890579/myworkshopfiles/[/spoiler]