This method of overwriting files always has the danger of human error (so does scripting!).
The best method of syncing would be using scripts and a wi-fi or internet connection to your desktop. Then you click a button and the two files are synced (modified data in records or new records added). GoZync has a plugin for this or your could script your own synch.
iTunes when copying Filemaker files using the apps area offers the option of overwriting or adding as a copy (1,2,3 etc). A dialog pops up asking Cancel, Replace or Don't Replace. The logic is a bit unusual since Cancel and Don't Replace seem to do the same thing: close the dialog and do not replace the file.
So your only concern is whether or not to replace the file with a file of the same name and this is where human error can occur since you can forget which is the latest version or you can accidently click on the wrong button using the desktop instead of the IOS device.
Since you have to be connected via cable or wifi to replace the databases, creating a safe and reliable method of syncronizing them without swapping would be preferable. If you have multiple devices this becomes a nightmare of options and one that I am considering using related tables rather than field updates. Often you do not want to replace data in a field but create a new related record instead.