I am sure someone from TOSEC will reply, but I assure you nothing is removed at least for no reason:
1) (most probable) ROM was incorrectly named and is actually something else.
2) ROM was for other system (so it is moved there).
3) ROM was bad (not just few bad sectors but actually something totally useless).
I don't think TOSEC removes ROMs because some company requests so, as TOSEC does not COLLECT the ROMs just catalogs (and keeps checksums) its existence.