Okay, thanks. I just noticed the archive function on the device.
Of course, the downside to this is I will first have to redownload the entire library again. And then manually archive all those items one by one through the device interface. Quite a bit more bothersome than managing them from my desktop computer.
I'm a little wary of using the trash feature of the library as long as it isn't documented exactly how Kobo is going to deal with that.
Maybe I should try out the Kobo Desktop App?