Testing with Astron Belt and version 1.0 , it certainly seems like Daphne does NOT maintain high scores when you quite the game and then start it back up again.  However, there's a command line option that seems to suggest that Daphne does preserve high scores.
From the Daphne wiki:
-sram_continuous_update  Saves the static RAM after every search so that if Daphne is terminated improperly, high scores are preserved.  
Does anyone have Daphne maintaining scoreboards from run to run?