UPDATE: Just for anyone still listening--I don't want to give out bad info. Calibre does indeed use the original source file. There is the option to use whatever ones are available, but the default seem to be the original.
I checked the input option in the conversion dialogue on several files, and saw that when an epub was the source, or, say, a .zip--that was the default for a new conversion. In my case, my
older books, when reconverted, multiplied those metadata headers, because at some point I lost my old Calibre library folder (can't even remember why) and reconverted from the file copies I had--all of which were .mobi files, of course. I had forgotten this until I reviewed.
Mark another one up for "user error."
Calibre was doing what was most logical all along. I had simply forgotten I no longer had a lot of my old source files from epub days.