Thank you for your post and I apologize for the late reply.
You should quit FileMaker Go when connecting to iTunes. Then, you can move the file from iTunes directly to the Desktop on your Mac. You should then be able to open the file with FileMaker Pro and see your changes. If you make any new changes in FileMaker Pro, then copy it back into iTunes and sync it back to the iPad (or other iOS device).
When you tap sync, the database file will move from the Mac to the iOS device (iPad). To copy the iPad to the Mac, just drag it out of the FileMaker Go directory in iTunes to the computer (Desktop or any folder).
Let me know if you need additional clarification.