Migrating to JIRA 4.4 is now complete. It has't been without hickups however :
JIRA 4.4 en Fisheye 2.6.0-2.6.3 don't get along when using trusted authentication. You get Seraph errors : Error handling trusted applications authentication attempt:BAD_SIGNATURE
Make sure the user that is authenticating the application link (and managing the JIRA project) has read errors to Fisheye projects. Else you can't link you repo to the JIRA project.
Make sure you have adequate backups before attempting to upgrade. Without them, it's a one-way ticket of something goes wrong.