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Good, Bad, mildly objectionable, KOReader will likely still be able to display the text in the file using one of its two reader engines Coolreader 3 engine (cr3) or the MuPDF based engine. Although there are those at the Github project who want to take the User Interface (UI) in a more graphic and data collecting direction, so far any feature that requires extensive "processing" of the files, can be optionally disabled. There is currently no check on the "quality" of the book format, of the file as it is added to the file structure, just the normal checks that it is a structurally sound file with one of the many extensions that the KOReader reader engines can handle. (Some extensions that could be read, are not normally implemented, but can be added.)
There is no special treatment that differentiates between files for ebooks bought from Kobo and those acquired elsewhere.
Luck;
Ken
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