Hi, Chet.
What you're seeing is that the Dock actually stores its application references, internally, as Aliases. If your backup drive is named differently than the source, and is available when you try to "use" the alias, it'll "find" the original file by volume name and path, and thus open the "wrong" one.
To resolve this kind of thing, you'd want to rename the backup volume to the *same* as the source volume before booting from it (Smart Update it first just to update the backup). Then, it'll see the boot volume before the original, and the aliases will resolve to it instead.
Regarding a Safety Clone -- yes, that makes sense, since many (many) files -- including symlinks -- aren't copied when doing a Safety Clone. That makes sense.
Does that help to explain?
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--Dave Nanian
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