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I've only used the Merge PI a few times and it does work as advertised: the selected and arranged files are merged into a single epub.
What I do to each of the epubs before merging is to make sure that
1. The files are arranged into folders
2. The text, style, and images file names in each are unique. I usually use a 01-, 02-, prefix for the first, second, etc. epub.
My experience is that if the epubs have the same file name then the PI generated a file name which I find confusing. Might not bother others
The PI also has some nice configuration options that you can us to 'tune' the result to your liking
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