Mongodb – Upgrading Mongodb from 3.2.6 to 4.2. Which is the better way to do it

Yes, just db.system.users.remove({}); for each database.

It seems a bit harder to drop the system.users collection, see: https://jira.mongodb.org/browse/SERVER-4302 but it shouldn't hurt anything if it's empty.

The authentication part is enabled when you run mongod with -auth, so don't put that in your startup script or config file (comment out auth=true, or put auth=false if you're running 2.0+).

A mongodump and mongorestore (or a similar script to accomplish the same thing) to backup and re-import the data is the most straight forward way of doing this at the moment until SERVER-6063 is implemented.

The only other option I can think of would be to move all chunks to a single shard, wipe out the sharding config for the collection (effectively unsharding it) and then do the rename on that shard. Once that was complete, you could re-shard the collection.

This would be:

1. Dangerous (messing with the config meta data is always a bad idea)
2. Unsupported (if you get into trouble, it's probably up to you to fix it)
3. More complicated (since the first recommended thing to do would be to backup your data via mongodump)

As one other alternative - can you move everything else (perhaps unsharded) out of this database? Obviously this would not be helpful if you have other large sharded collections in this DB, but just wanted to make sure it was considered.