Hi Benjamin,
I believe you can point the Workflow Manager 10 post-installer at your 9.3.1 database, and it will upgrade the database in place.
The JXL export/import works well for many things, but I don't believe the 9.3.1 JXL export function will include the information about existing jobs in the JXL file. (This has changed at 10.0.) So none of your old jobs will exist in the new database after you do the JXL import.
Either way, I'd recommend making a backup before upgrading and/or running a quick test with a test DB, just to be on the safe side.
Brian D.