There is a backup function in the settings so you can save all your playlists every once in a while.

I will further look into this issue, but as of now I haven't been able to recreate this problem on my device.
What device do you have?
If it happens again please let me know (with the steps if possible).
Sorry about the inconvenience and thanks for reporting the issue.

Force closing apps on the Kindle (if that's your device):
Go to Settings (little gear at the top right) -> More -> Applications
Filter to show Running Application
Click the ones you want to close and choose Force Stop