Unable to start mongodb as a service - Exception; Collection does not have UUID in KVCatalog

The problem can be solved by:

1. Backing-up all the databases (using mongodump)
2. Removing every file in /data/db, due to their incompatibility with the newer version: rm -rf /data/db/*
3. Restarting the MongoDB service
4. Restoring all the databases (using mongorestore)

I have met similiar problem with admin db, when upgrade from old mongodb 3.4 to 4.2.

Solution is to mongodump all dbs and delete /var/lib/mongodb, then mongorestore all dbs back.

STORAGE  [initandlisten] exception in initAndListen: MustDowngrade: Collection does not have UUID in KVCatalog. Collection: admin.system.users, terminating
2019-09-24T21:59:55.274+0000 I  NETWORK  [initandlisten] shutdown: going to close listening sockets...
2019-09-24T21:59:55.274+0000 I  NETWORK  [initandlisten] removing socket file: /tmp/mongodb-27017.sock
2019-09-24T21:59:55.274+0000 I  -        [initandlisten] Stopping further Flow Control ticket acquisitions.
2019-09-24T21:59:55.274+0000 I  CONTROL  [initandlisten] now exiting
2019-09-24T21:59:55.274+0000 I  CONTROL  [initandlisten] shutting down with code:100

The cause of problem: mongodb 4.2 will add userId with UUID value in system.user collection. Hope this will help.

When upgrading another mongo db, I met the exact same problem as yours on startup_log, it seems I did not stop the mongodb when delete the /var/lib/mongodb folder, after stop mongod and delete the /var/lib/mongodb and upgrade to 4.2, error goes away.