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@mjh215
I've tried this and had no problems. Can you verify this behavior with a small Word File. One page should do.
With large files some books take a long time to build. I've seen this with IMP and especially ePUB. Because the books take so long to make, it looks like the books where never made but in reality the process is still running in the background.
Chances are by the time you decided to run the tool a second time the first book was getting completed. The 2nd instance does no harm it just overwrites the first book.
With a small book the process is fast enough that you will not experience this.
=X=
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