For your primary, create a calculated field with the calc get(uuid) for ipad and server solutions. Set as unique value. Set as do not replace existing. This will ensure no duplicate ids.
Your script can perform a find for the found set on the ipads after the import and then run this Delete All Records
You would want a script in there to verify the import has occured before deleting from the ipads.
Have you looked at the existing sync frameworks available?
Seed code has a free version that sync one table and it can be downloaded here :
Even if you do not purchase it is a great example.
A free solution that requires FMS which you state you have can be downloaded here :
I want to add another solution which I am currently developing. It synchronises FileMaker Pro, FileMaker Pro Advanced, FileMaker Go, FileMaker Server as well as FileMaker runtime solutions. Feel free to try and provide feedback to the recently published demo: FileMaker Sync without plugins without FMS (http://www.filemaker-sync.com/)