A solution I've been working on is something that I'd like to see on FileMaker 13 with all of it's new features. Currently it is running on FM12 for desktop and iPad, one of the features I implimented was a update function for the iPad. For example, if a local copy on the iPad has a lower version number than the server copy, the user is promted for update with a yes or no option. Tapping no has no effect on the iPad's data while yes will import all records to the corresponding tables by pkID.
I pulled a copy down from my 12 server and proceeded to upload it to the 13 server with no problems at all. I then remapped the import process for the offline copy and copy and pasted the script steps into the online version, double checking that the import won't go to the wrong file and that the correct accounts were being called. When I ran the update again on FMGo13 the import to compare version numbers failed, and the database proclaimed that there were no updates available when I knew just before I launched the file the online copy had a higher version number than the copy on my iPad. So I took the copy off and ran the import again on the desktop, this time the database recognized that a update was available. This is very confusing since I know the first import script step is the problem, as it is either not connecting to the online file at all or something else has gone wrong.