Also, Kobo software is picky about the fact that the used file extensions must match the file internal format. Hence, file extension .CBR (RAR compression) and file extension .CBZ (ZIP compression) must correspond to the file contents. I've seen myself that mismatched files did not show up in the e-reader.
You can check this with the aid of for instance the Notepad++ editor whether the first 2-4 bytes of the file (=magic number) corresponds with the extension:
- CBR files must start with Rar!
- CBZ files must start with PK
When needed, adjust the file extension to the real file internal format.