The backup copy is not a perfectly identical replacement for the original disk.
Dock items point to the original disk, not to items contained on the backup copy.
(I suspect similar problem with aliases in general, but have not checked it yet.)
I can understand why items might be copied exactly, and that is a desireable feature.
However, there should be an option to modify Dock items so that their references behave as one might wish and expect- for example, if user wanted to make a backup copy to replace an original.
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Extreme Q