Warning this is pretty speculative.
I do know that delete book on the Kobo doesn't seem to really work on Calibre sideloaded books. It seems to delete the connection to the sqlite Db, but the files themselves remain. I have no idea if this can be a problem, at some point, or not. I also have no idea if deleting through Calibre first is a good idea
. I have gotten in the habit of using Calibre to delete the books I load using Calibre AFTER I do the delete through the reader.
I also noticed that it works better when I only send a few books to the device at a time--say 5 or so. This is outside of my area of expertise, but I sorta assume that loading the books and making the Db connections for them is processor intensive, given the hardware--particularly on Kobo-1. YMMV