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@Brett Merkey,
EpubMerge is working fine for me in Calibre 4.5. Your Calibre version 3.42.0 is quite old.
None of the GUI plugins I tried allowed disabling, but file type plugins did--I'm not sure what the details of plugin disabling are.
If you run Calibre in debug mode (Calibre Preferences drop down), it might give some useful output.
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