Sorry, I know nothing about 'Epubor Ultimate'. As you are starting to use calibre, take a look at the tools supplied by Apprentice Alf. Obok is one of them. If the books come from Kobo and have been downloaded to you PC using the Kobo desktop application, it will be able to help.
Of course, if these are the 100 free books given out by Kobo with one of their early devices, they were probably are all books whose copyright had expired. If so, you can probably find them on the web somewhere. Project Gutenberg, the MobileRead library, lots of other places have these books. And if you need a list, I know there was a thread discussing them here. It's from a while ago, so you would need to search.
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