When reformatting something large, I convert to RTF, edit in Word, save as HTML, then drag-n-drop into Calibre and convert to epub. Below are the instructions for Word, on a PC and not a Mac, so your word processor may be different.
If you turn the formatting icon on, (It's on the "home" tab, and looks like a backward "P", a 'paragraph mark'.) you can see the formatting marks. You can look for the problem areas, and search and replace those.
Open the "Find and Replace" option, and down at the bottom open "More", and then "Special". There are about 20 formats you can search and replace. You can do them all at once, or one at a time, which sounds like what you need to do if you don't wan them all changed.
I'd keep a good copy, then play around with the settings and see what the results look like. When I collected fanfic off of Live Journal and other sites, before the fanfic plugin, I 'fixed' a lot of stories this way.
Just don't forget to save them as HTML before reloading them in Calibre.
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