If I add or remove any verts to any mesh it breaks the mesh near the waist between the top and the pants, it seems like the link between the top mesh and the bottom mesh is confused and is pointing to verts that are not the top ring. I'm too new to meshing to know why or how to fix it and everywhere I look online there are only tutorials for moving meshes from other things into the sims or franken meshing, I just want to make some small edit to an already existing mesh by adding more detail (using the knife tool to add more verts and move those around).

Is there any way to reassign the connections? is this even the problem? The tools I'm using are just blender/paint.net/sims4studio.

Not sure if TS4 clothes are dependent on morphs (I think so?) but if so that's probably where the problem is. Vertices are numbered, morphing depend on the exact vertex count (the vertex on the morph targets the vertex of the same number on the main mesh), and removing vertices from the main mesh will cause the morph to get confused. Messing too much with the mesh can often also cause the UVmap to get messed up.

Would help with a picture of the problem, or the file from the mesh program that shows the error, though.

The stomach is all messed up, and this happens whenever I add or remove even one vert.

Still Hard to pin-point exactly what your trying to do though. But if it is a top, with a naked belly, it's better not to touch the very bottom line vertices as they by default are perfectly aligned to make it appear that it joins to a bottom mesh.

Above that you can edit, add, modifying etc. but if you move things to much/or add things, your weights will be out of alighment or unassigned, and you got to fix these too, or you see all sorts of werid behaviour when you preview it in the game.