This might help you. I was never able to get our data to sync back to the map. Tech support said they recommended less features be collected before each sync, which isn't always an option. Here's what I did to recover the data.
Steps:
1. Pull data file off of iPad using iTunes
2. Make backup copy. If you have a lot of pictures this can be large so make sure you have enough space. Our folder was about 3.5 gigabytes.
3. Download SQLite maestro or similar SQLite viewer
4. Query the duplicated records based on "gdb_from_date" and "gdb_to_date" fields.
5. Then use the python script referenced by Tech support to export the XML and load back to a geodatabase.
It's a workaround if you can't get the data to sync, but can be a bit tricky if you're not familiar with database management tools, so I'd recommend a backup first.
Hope that helps!