FF3SE-M

The only thing I would say against that theory is that The problem doesn't seem to be dependant on how many sprites I load. It cuts off espers mid-way through starting in the back. If it were a max number of "big" templates, then I should hypothetically be able to import all of the 128x128 sprites on the monster side and start seeing them disappear instead of the espers, but that wasn't my experience. Even unedited sprites disappear.

It looked to me almost like maybe it didn't know how to load data after a certain point in the ROM so SE loads blanks then correctly saved those blanks over the good data. Granted, I didn't do a lot of testing with inserting sprites near the end or middle of the monster list, I worked pretty much entirely at the beginning of monsters and end of espers.

Edit: We could also test it by loading a bunch of 64x64 sprites over the 32x32's.