Your stage progression is saved each time you prestige. If your game crashes you will be loaded back to your last prestige. Unfortunately, there is no way to recover stage progress lost between prestiges and active perks may also be lost.

Note: All in-game inventory (Artifacts, Pets, Crafting Shards, Equipment, etc.) is saved as soon as they are added to your account and will not be lost if you are to experience a game crash.