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Just a last update to this.
With more experimentation and reading I learned that the _foo_ format is used by Markdown and Textile markup languages to signify italics or emphasis in a text file.
I have a few .txt files with this markup in the document so I found on Calibre in the "Preferences:Conversions:Input Options:TXT Input" a pulldown box under formatting style to select either Markdown or Textile formatting (instead of auto).
Either of these options converts _foo_ into foo as the txt file is converted to epub (or presumably any other format).
Hopefully this will save someone else a little time on this but I have learned considerably nonetheless from nattering over this problem.
Archon
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