Where does the main/alt flag come from? I imported my guild with some 260 toons and set the main/alt for the initial import. Im now going back to update the list w/ new levels, etc, and it seems to want to set all the account to main by default (well, most, some are alt, but bottom line i rather have it left alone after the initial install.)
It should be set on each profile of each character.
Admin > Characters and Accounts > CharactersOnce they are set an import won't change that status as far as I have every seen.