Hi msummers,
You can disable synchronisation information (the dwsync.xml files) per/site in Dreamweaver. Open the site in DW and:
DW Menu bar > Site > Manage Sites > select your site > Edit > Advanced Tab > Uncheck the 'Maintain synchronization information' checkbox
Click OK to the info/warning box. This will disable synchronisation and also remove the existing dwsync.xml files. You can re-enable it (if you want to) later.