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Getting rather weird. It only happened on my Intake library. So I created a new library copying the structure of the Intake library and copied the contents of my Intake library there. After the copy, I could happily Modify ePub the contents of Intake2 without getting the error message after clicking on yes. I then deleted the original Intake library, created a new one after deleting the contents of the Intake directory, copied everything back from the Intake2 library and no issues running Modify ePub.
When I was playing with my original Intake library after moving the contents to Intake2, I copied 5 files from my Main library and they came up with the same error message. So something in the library or it's structure caused the issue but, as the old sign I had above my desk at work said, We don't believe in miracles, we just depend on them.
I've attached my Modify ePub configuratin screen and the calibre debug error logs. Once again, thanks for your help and feedback.
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