By this point, you may have a borked Db on the kobo. I think what I would do is start over.
By this I mean remove any book files or book folders you have on the root of the kobo and do a factory reset. As a factory reset does not seem to fix a messed up sqlite Db, replace it, as well as the images and kepub files following the directions in the
sqlite replacement sticky
When that has happened, you will now have your preloaded books as kepub files, rather than in the Db itself. Those should now be the only books on your reader.
Test your machine by adding in some books you have already purchased or free books from the Kobo site. Add books into the main memory through sync, as ePUB through Adobe ADE, and as ePUB via Calibre. If everything goes as it should, do the same things but add the ePUB books to an SD card you absolutely know is good, even if you have to buy a new one to be sure.
Finally, try adding the comic books you have converted to ePUB.