What database are you using? Why do you want to export users and not use the same database and upgrade to 3.9.3, or connect to the same database from a fresh 3.9.3 installation? Openfire should handle (ideally) the database upgrade during the first startup.
Export plugin hasn’t been updated for a long time, so it may not be working correctly. It is also only exports users. I think you are better with using old database than exporting and importing limited data.
How is hardware related? Do you mean you want to install MySQL on a new server. I think there is tools to dump databases and import it to a new installation.
Using your database tools you can drop tables with the conversations.