Another thought,
Although I am not a programmer by profession it seems to me that it is the act of exiting the Thinking Rock iPhone app during a sync that results in the local database being wiped.
The first time this happened to me was when I had realised I had not turned WiFi on on my iPhone before I started the Sync. My natural reaction to this was to exit the iPhone app using the home button, turn WiFi on and then return to the Thinking Rock app to start the sync again. However when I retuned to the TR app all data had gone, everything not just my recent thoughts. I had the TR app crash to the home screen about 30 minutes ago during a sync and again all data was gone. So it appears to be that any attempt to exit the app whether by design, using the home button, or by a crash while a sync is trying to run will result in the loss of all data. Basically if the TR app cannot get a connection to the external database over WiFi for what ever reason it just sits there, saying it is syncing. It never times out and offers a way out of sync mode. So you only option is to hit the home button and that deletes the local database.
Anyhow, hopefully this can be resolved.
Alan M