Hi Mike,
Are you editing the shipping CSS and JS files?
If not then you should be ok copying mine over yours, since your stuff will remain untouched.
The scripts folder is the most important one, and this has to be tightly syncronised with the generated CLW code.
The styles folder is the next most important because I add, or tweak, styles from time to time.
Ideally Images should also have different names to me, but this is less of a big deal because missing images are both obvious, and don't "break" the site.
So the bare minimum is to copy the scripts & styles.
Cheers
Bruce