The problem is that when you're using Copy Newer, complicated data structures (like your SyncServices data) aren't maintained in a way that's restorable, because data isn't ever deleted, so you can get lots of extra links, etc... as you're seeing here.
Smart Update is really the way to go if you want to be able to restore easily - and a full backup, of course, not just User Files.
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--Dave Nanian
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