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EpubMerge operates on a principle of changing the input content as little as possible.
So each time you merge two (or more) epubs, each is placed in a numbered subdirectory so that files with the same names don't conflict and relative links (../style.css etc) work without changing anything.
Adding many chapters one at a time over and over is not the best way to use EpubMerge. I would instead suggest that you collect all the chapters together and merge all of them in one operation. Every time you call EpubMerge on an epub you've previously merged, you get an other layer of nested directories--that just the way it works.
There's going to be a limit to how deep you can nest dirs in a zip file; I suspect it may vary between devices/implementations.
However, EpubMerge also as the ability to 'UnMerge' a merged book, essentially giving you the pre-merged epubs back again. Assuming you didn't turn off the 'Keep UnMerge Metadata' option before the merge and haven't processed the merged epub through another tool that discarded the 'extra' files.
So, if, for whatever reason, you have to add one chapter at a time, I would suggest that you first 'UnMerge' the existing book, then make a new merge with the prior chapters plus the new one.
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