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It is processing 50,000 books. See my previous post about that. 5 hours represents only 20% or so of how long Calibre would take to do a "real" copy.
The Job Log will tell you if something is wrong.
To allay your fears, open Windows Task Manager, and watch the Calibre process statistics change for CPU and memory. You may have to tell TM to show you all of the processes it has to see everything.
DaltonST
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