Unfortunately that's what I already do, and it doesn't work! Well, not very well, anyway!
The problem seems to be that the filename given to the messages contains the name of the computer to which it was downloaded. So if you have synced the machine once, and then VERY LABORIOUSLY deleted all the duplicates by hand, the next time you sync, it duplicates them all again! Presumable the "remove duplicates" doesn't work because of the difference in the filenames assigned by the different computers!
And why there is no "export" to a standard file format completely escapes me! This is the kind of "vendor lock-in" we expect from Micro$oft - not an open-source application!
(Rant over - honest!)
So thanks for the pointer, but its what I'm already trying. It works to a degree, but creates as many problems as it solves!