By read these two threads, I found out that all the edited continental competition has to be create the competition again from scratch in the editor, removing the existing competitions entirely instead of just edited them. By create competitions from scratch to include competitions rule (which I want substitution rule to change to 5 from 12 and new squad registration rule from AFC champion league) and doing so could cause breaking the coefficient/qualification system.
I already had pre-game editor, but I cannot see which part of continental competition editor file that would cause breaking the coefficient/qualification system and I don't know how fix this.