How to properly enable server-side encryption on existing multi-user install?

Do you use external storage? For that purpose the server-side encryption was designed. If you don’t use it, the benefits are very little and you potentially add a lot of complexity.

There were a few problems with Collabora (most of them resolved): Collabora not working with encryption - #36 by just
Also I’d look into how the master-keys are working in case someone forgets their password, and how to restore data from backups. There are a few topics here on the forum and github.