We had the same issue. i could fix it by running the db migration multiple times until there where no migration left. between the runs we also had to run some manuell commands:
gitlab-rake db:migrate
gitlab-rake gitlab:background_migrations:finalize[CopyColumnUsingBackgroundMigrationJob,ci_stages,id,'[["id"]\, ["id_convert_to_bigint"]]']
gitlab-rake db:migrate
gitlab-rake gitlab:background_migrations:finalize[CopyColumnUsingBackgroundMigrationJob,ci_builds_metadata,id,'[["id"]\, ["id_convert_to_bigint"]]']
gitlab-rake db:migrate
after the migration we had to reboot our server.
The manuell commands where written after the db:migrate command failed.