Playlists seem to randomly go away. Sometimes they will persist for days. Sometimes a day. Sometimes not even across a single reboot.
I have looked for a relative Exaile directory to delete the contents in case there was a corrupt cache or something. Can't find it. Did not see a setting which points to a "directory for Exaile to use".
Running Exaile 0.3.2.2 on Trisquel 5.5 (an Ubuntu derivative) with MATE GUI (what used to be GNOME 2.x) on a 6-core AMD-based machine.