I havne't checked but I expect the actual Formation (Arrows, positions, role select, defence) to stay the SAME in ML since now edited stats also carry through BUT... lineups work a totally different way in this game.
In ML, AI uses its own intelligence to pick your startin 11, not the ones you set in Starting lineup.
But check to see if actual formations stay, half the times if those players have their realistic values, AI will pick something very close to real life starting 11 anyways.. I had this happen after applying my own data file and was very fun to see
@Shevchenko, do you mean if you transfer Abbiati to "Free Agent" section and then lets say he moves to Inter??

hahaha.. well then you can go to "Free Agent pool" and transfer him to another club.
Hope this helped.