So I'm doing some conversions.

Basically I wanted to cut open an existing model I've modified with the Boolean tool, which is a picture frame and deleted the vertices to fill in the gap with textures, but when I import it to Milkshape, the modified vertices aren't registering. I tried importing to SimPE first but it gives me the "problems while parsing file" error and it looks broken.

It's not like that when I port the .OBJ file into blender, as it retains the vertices.

First meshed in which program?

If you haven't properly converted the Boolean to be part of the mesh (whether it's addition or subtraction), the boolean action usually only exists in the program you did it, because Mikshape doesn't have the same tools and can't translate it.

You have to add or subtract the mesh part/boolean, and preferably make sure there are only square or triangular polys (Milkshape can have issues with polygons where there are 5 or more sides/vertices - not always, but sometimes).

The "Problem with parsing file" error often comes from having used the wrong export settings in the program (common issue with OBJ files in Blender or Wings), or from multi-sided polys Milkshape has issues reading.

I first meshed this in Blender, which was ported from a Sims console game. Looking at the sides, it turns out there are more than 5 vertices in some parts. Is it recommended to use the Knife tool to make them into triangle or square polys?

On a similar note, I also noticed that the boolean parts were untextured, so I deleted the untextured faces so I don't get any missing texture errors.

EDIT: I used the knife tool to condense some polygons and it worked!