I had a crack at synchronizing, using Import. I put down my lack of success to my scripting ability but I was wondering if its just not possible to do it that way?
The idea was to find only the records that had changed and flag them in both files, then import the found records from one file - (update records found in current set adding new records) to the other file showing all records and then do the reverse.
I had a few problems based on the unique field in both records and new records seemed not to get transferred all the time. I was wondering if I should pursue fixing the unique ID field or just drop my idea of using Import for this task.