Playlists are stored in the database. So it might be a good idea to export them and also make a backup of the Subsonic.db folder to another location.
There have been issues reported that while upgrading the database got deleted.
According to the installation instructions "
If you're upgrading an existing Subsonic installation, you don't have to uninstall the old version first. In any case, the existing Subsonic settings are preserved. After installing and starting Subsonic, open the Subsonic web page on http://localhost:4040. "But I guess it's better to be safe than sorry.
I would also like to point out to you that according to Sindre a newer version (6.1) is soon to be released.
http://forum.subsonic.org/forum/viewtopic.php?f=4&t=17168