AFAIK the game section of world.dat only has the league id and not the subleague id, so if in game setup you move one team from a sub-league of 6 to a sub-league of 4 the schedule should still work. You may find that one team in one sub-division then has a high number of interleague matches.
The best way to do this would be to set up 1 sub-league with two divisions of 5, and then in game setup, add a sub-league and move 5 of those teams across. With a balanced schedule at start-up it should work fine.