After a long genie fight, I quit 100 Rogues, and restarted it a bit later.  I chose "Continue", waited through the usual loading screen, and found myself at the beginning of the genie level, without any of the progress I'd gained in the genie fight (2 levels and 100+ HP and energy).

The items on the shop also changed.  (On the bright side, the shop now has a +2 CD's Griffin Slayer available.)

100 Rogues needs to save far more often than it currently does.  Ideally it would save after every action, but at a minimum it should save whenever switching away from the game or exiting the game.