Thanks for the additional info rashkae.
I seem to have figured everything out. Managed to do the epub->epub conversion which fixed issue with covers, fonts, and margins.
However, there was one undesired effect. Many of my original epub files seem to have the location of page breaks stored. Ie. no matter what my font size, a book I am reading will have 420 pages on my Kobo device, and will show when a page changes on the right margin (seems to be some correspondence with page numbers from a hard copy of the book). After I do an epub->epub conversion, this page break information seems to be removed. In other words, the number of pages shown by Kobo changes depending on the font size.
Does anyone know how to do the epub->epub conversion without affecting the page numbering in this way?
Originally Posted by rashkae
Calibre now creates a backup of the original epub, which it will use on any further conversions (in case you need different tweaks/options for desireable results.).. You can also restore the original from the Meta Data screen. I would nontheless advise keeping a backup of your books as they were before bringing into Calibre. It's a fairly sophisticated program, and it's relatively easy to make oopses.
*Edit* Not discussed here, but it's worth mentioning that using the "Tweak Epub" command to manually make changes to an epub will not back-up the original, but works directly on the current file.