I added this statement: "Keep in mind this is a demo app subject to change in the future. You can download your docs at any time." as a warning to anyone who might be using this site with expectations that the data will be persistent.
Ultimately I figure the only solution for a production app is to either do a better job educating users on these issues, or scrap the offline persistence selling point entirely (and just rely on it as a cache).
What did you end up doing with your products?