I wouldn't go that far as saving everything as txt, you will lose italics and other formatting that you might appreciate, all things being equal.
I'd say that if you can't get it looking up to your normal standards with a simple conversion in Calibre or maybe a tweak or two before converting to your favorite format, then let it go... But I'd always take a few minutes to give prettying it up a shot. I won't spend an hour on it again though.
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