mmm ... okay, I'm trying to figure out if you've got the kepub versions of your ebooks on your device, which may or may not be relevant.
In the device settings, Manage downloads, last option: "Once you've marked a Kobo book as finished, remove the download from your ereader to free up space" .... isn't ticked is it?
(btw, the time difference in my reply is because I live in Sydney, Aus)