This problem has been solved since Mendix 4.1.1, see the release notes:
Ticket 13760: Fixed not-null constraint violation database exceptions while migrating from Mendix 3 to 4 in case of some database corruption.
I am not sure where you could find it, but for one you need to keep in mind that during the conversion you are going to need a lot of space. Because id's are handelled differently in 4 all database id's will be converted and this process takes up quite a bit of disk space.