eschwartz, your reply makes total sense. However, the "line breaks" not having a <br> tag in the html comments are not <br>'d by calibre during the S&R process. This only occurs with the comments that already contain <br> tags interspersed within the sentences from the downloaded metadata. This means that calibre must be ignoring the <br> tags when searched from the edit metadata dialog.
I'm super happy that the S&R removes all the other html junk and will live with manually editing out the <br> as necessary, I just thought that I was doing something wrong or there was an easy answer I was missing.
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