Hi there and welcome to Zune Thoughts.
To answer your question, I guess it depends on how you've set up the sync. Have you right-clicked and selected SET UP SYNC then un-checked the box for "Sync Automatically"? That will give you more fine-tuned control over what syncs and when.
If you want to do the automatic sync, but you also want it to update the files whenever you updated any piece of metadata...well, I'm not sure how to get it to do that. I suspect there's no way to force it - I suggest you finish editing all your metadata (which can take a long time, I know) then erase the Zune and do a re-sync.
If that's not what you were asking about, please provide more details and I'll try to help....
Auto Synchronize with Large Music Collection
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Hybrid Mode
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