Please contact Qlik Support. The likely fix based on the symptoms is to run a script to clean up one of the tables.
The explanation (based on the symptom of some of the migration status rows being blank) is:
In the database there is a table called AppStatus that keeps track of the migration status for a specific app. A variety of methods can cause the database to become misaligned (multi-node, use of APIs, etc). That will give us a situation where we have one or more AppStatus entities that is pointing to deleted or non existing app entities. After an upgrade is done, the seeding process will again fail when trying to update entities that are pointing to deleted apps.