I figured it out. Placing this here in case anyone else is looking for this fix and finds this. I couldn’t find this anywhere in relation to vrchat, but it’s a relatively simple thing for unity.
Prefabs. The reason it’s not saving is because you have to unpack the prefab, and in order to save it as a new prefab (not using “reconnect prefab, that will just reset it) you have to drag this new asset from the hierarchy window to the assets window, where all the files are. Also, try using FBX converter, so you can directly turn your object (avatar) into an FBX which can be more easily rigged using the SDK. Hope my pain helps someone in the future.