I think we just ran into the same problem. Here was our sequence of events.
1. User collected data all last week (10/5-9) offline using an iPad air
2. The user returned to the office on Friday (10/9) and connected to wifi but did not sync immediately.
3. The user went to sync and noticed that the map was no longer listed as being on the device
4. I connected the iPad to the iTunes today manually removed the existing folders.
5. there was an empty folder on with the users login name and an update time of 2:34 on 10/9 or just after he connected to wifi. But the folder is now empty.
When I talked to ESRI tech support on Friday they assured me that they had never heard of this issue before and it must have been user error or a hardware malfunction. Based on what I'm reading here I think the app update may have removed the data.
It would be great to get clarification on this from ESRI. I know have a field crew and project manager with little confidence in the collector app working.