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Yes, you should be able to, as the path of my SD card when connected via AS to my Vista machine is "Computer/HTC Prophet/Storage Card/".
Obviously, replace HTC Prophet with whatever you've named your Axim, and you should be able to copy the files w/o having to make duplicates of all media files in the mobsync'ed folder first.
Although, I simply use the fantastic Syncback SE for podcasts in the iTunes podcast folder, while I use another Syncback profile to sync the contents of my SD card sans the podcast/vidcast folder, as that is already synced with the iTunes folder. Both profiles run at lightening speed using the built-in card reader - much faster than the wired AS, and much much faster than Bluetooth AS.
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