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It's normal for KOBOeReader to be empty after a factory reset. These files will be created on the first boot.
You should not touch the recoveryfs, if you modify that factory resets will no longer work.
As for the rootfs you could check if there is a file usr/local/Kobo/sickel - if the factory reset worked it should not be there.
If nothing else works you might need a Kobo Glo SD card image from someone else.
Did you install firmware manually and picked the wrong markX?
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