@GeckoFriend - I can guess what the problem is, it is another permutation of interactions between different options (and obviously a bug in the plugin).
You have ticked the "Add/replace jacket" option at the same time as "Insert/replace cover". If it happens to be a book that didn't previously have a jacket, then the code will hit the error you see.
To avoid the error, just run Modify ePub twice - the first time without Insert/replace cover ticked. I'll push a fix tonight when I get home to verify it is the case. I don't add jackets myself so didn't catch it.
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