It's hard to help when I have so little information to go on.
I'm also not an expert. I've never actually done this myself; I was just describing how I would do it if I ever had a reason to try.
Have you tried opening the HTML files in a web browser? If so, do they look OK?
Have you tried dragging the HTML files into Calibre's GUI and proceed from there? Maybe that'll give you an idea what's going wrong. (You can batch convert through there too.)
If you still have trouble, try asking in the calibre forum, since if the HTML conversions wine fine, the issue is with calibre.
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