I would put that sort of issues on whatever you used to do the conversion ;o).
Regardless, the important thing is that you found something that works for you without too much hassle
.
For context and other interested readers, I wrote a couple of scripts to do that (from sane source ePubs/CBZ, e.g., Humble or liberated Kobo store) for my own use-cases:
unpack &
repack.