Having to upload whole sites after upgrading Freeway.

I have again updated Freeway Pro to its most recent version.
Yet again when I go to upload an updated website I find that the whole thing has to be uploaded again and not just the updated files within the website. This is particularily frustrating given that there are some quicktime movies embedded in some Quicktime Actions. Is this normal?
How can I link a quicktime action to a quicktime movie so that I can upload the actual file using say Transmit?
Hope that this makes sense!
Any thoughts?

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