Forgot to unparent armature while editing mesh, how to fix deformation? This problem is a bit tricky to put into a search engine...
Anyways, hello!

I've been working on a relatively low-poly human model for a while now, teaching myself how to rig and model and such... Well, I got a little carried away and forgot to unparent the mesh while I edited it. The result is... confusing!

When going from edit mode with the proper shape to object mode, the mesh deforms in some bizarre ways. The left foot merges with the right foot and they both try to revert to how they looked before changes but with many new vertices. My question here is how to get the armature to register the changes!

 

Here are the actual bones they should be fitting to (I also edited these while the mesh was parented. Big oopsie.)



I tried to fish around for a solution but the mesh remains deformed in Object mode even if I unparent the armature or disable it and the bones do not want to re-auto weight themselves. The deforms stay in place even if they have an empty vertex group! Also, I can't weight paint because the deformations appear in weight paint as well.

I also have an animation in the Dope sheet, I read somewhere that that might be important.

I would love some help from someone who knows what they're doing
I downloaded your file, the issue is indeed from Shapekeys.
The reason why you can't see them is that you did a word research of your shape keys, and none of them correspond to, so they are hidden. Sympy remove the research and you will get your shape keys displayed :



Then, if you want your modifications to be definitive instead of shape keys, you simply have to select and delete every shape key, keeping the shape you want to keep as the last to delete. Here I did the manipulations to make the Key 2 as definitive shape: