Yeah, you can't have too many backups.
You don't say what it's currently used for, except for "office-functions", if it's used as a mail-server, either zarafa or regular, you'll run into trouble no matter what you do. (The user id's won't be the same), and if you run the script, everything will be deleted (as the data depends on the users.) Make sure you have a backup of the data as well.
Anyway, I actually had to do this yesterday on a real server as there was an error I quite couldn't get rid of, so I decided to rip out the guts and start half-fresh. It worked as advertised, except that the mail-filter module wouldn't work, it complained about something related to ldap-schemas. Uninstalling (even with --purge) and re-installing didn't help. What *did* help was running "/usr/share/ebox/ebox-unconfigure-module mailfilter"
That's a neat little script to fix otherwise "unfixable" modules. (You have to re-enable any "unconfigured" module in the web-interface.)
Good luck with the migration.
::Trym