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OK, a couple of issues I've discovered:
1. I had installed some new software (VMWare Fusion), with the app on the original disk and an alias on the Sandbox. I created the alias manually, so it wasn't a symlink created b SD! When I copied the Sandbox back to the original disk, it was copied as an alias (pointing to nothing, of course!), so I had to reinstall the software. Not a big deal.
2. When apps permanently in the dock were opened by double-clicking on a file (say, a Word document), a second instance the app appeared in the dock. I needed to delete the old dock apps. Also not a big deal.
3. Office apps needed to "reinitialize" themselves, as if they had been opened for the first time. Also not a big deal.
We'll see if anything else develops!
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