you have to make the edits in the origin game to make the main structure legal, seems to keep and fix some substructure values between games,
for example i caught a cresselia in Shield max lair and sent it into shinningpearl, then i sent it back into shield, started editing in shield because i caught it here made it shiny, changed pokeball, trainer ID to make it fit with shinning pearl, then i sent it into shiningpearl and then HOME and seems to be working because the pokeball appears and the children info showing correctly, in both shield, shining pearl, even in HOME
then i tried to do the same with the original untouched cresselia, starded editing in shinningpearl game but this didn't show the pokeball and sword shield children data, (HOME game icons).
i didn't fixed home tracker so i am not sure about that...
seems to carry main sctructure while changing some substructure like the modified (pokeball, shiny, tid) in my case.