In fact, the installer will build a directory with JOnAS pre-installed/configured in that directory.
But you can keep your old JOnAS and config in another directory.
Then the best way to do, is to create a new database in parrallele of the previous one and just use it for the new version.
After that you might be able to migrate your data by import/export in XML from the previous one.
Regards,
Artenum Team