We stumbled onto two bugs: A missing repo (e.g. due to a move) causes the JigitIndexer to stop before indexing all configured repos. A missing default branch (e.g. due to misconfiguration) causes the JigitIndexer to stop before processing all futures (hence also stops before indexing all configured repos). See stacktraces in attached bug1.txt en bug2.txt respectively (note, I've anonymized the traces).
Jira: v7.9.1#79001-sha1:60970b Gitlab: 11.5.6-ee
Attached is also a bugfix that worked for us.
Best regards, Robert