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This is not so important as to go to extreme means to keep the custom metadata out. I just would prefer my comments not be in the epub files. Some might be useful, like if I have an associated audible file, but since we can't see them anyway without an epub editor, it doesn't help for it to be there.
I experimented before the above last few replies and I thought I was going nuts! Who would have thought something like "Update metadata embedded in the book when opening" would be even there much less the default. Once that is in there, I can't see a way to get the metadata out again short of editing the opf file. Even what you think of as the original epub is not if you opened it in the editor because of that setting. Furthermore, you're going to pollute at least one file to change the setting, since the setting is in the editor itself. I think I remember glancing at the settings and didn't see anything dangerous, but being a novice with Calibre it's hard to know what's going on. I probably didn't even get to the last line -- integration with calibre.
SO... Yes, after I figured out I was not going crazy and didn't touch the calibre editor any more and used sigil, the custom metadata is not written out with Convert Books. I'm not sure this is trustworthy though because it could be an "oversight" that might be "fixed" at any time, since the other methods of writing out metadata write it all out...
Thanks everyone!
Judy
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