The listing is not set to display file extensions. I think you would have found that the files were still all called .ePub, but had become associated with the ComicRack reader. The type column is showing what application is registered to use that file type.
The file association gets changed if you choose to open a file with a different application, and don't notice you have the option checked to always use that application to open that file type.
System restore would have reversed that, plus whatever else got reversed going back to the last restore point. The proper way to change it would have been to change the file association back to the original reader you were using for ePub books, was it ADE reader? Looks like the icon in your screenshot is for the regular Adobe reader.
Edited by Platypus, 30 May 2018 - 12:19 AM.