I just found the .submodule (forgot exact name).gitmodules hidden file, it has a list... you can erase them individually that way. I just had one, so I deleted it. Simple, but it might mess up Git, since I don't know if anything's attached to the submodule. Seems ok so far, aside from libetpan's usual upgrade issue, but that's (hopefully) unrelated.
Noticed nobody posted manual erasing, so added