Here's some info from the Kobo reader forums on MB that explain syncing, perhaps your I'm Reading folder is empty?
Create an account at the Kobo website, or log into your existing Kobo account. Click on your library. Unless you have done some fiddling already, all the books you have bought will appear in your 'I'm Reading' list. This is what will sync to the Kobo .
If you have some books you have read already and/or don't want to syn to the Kobo , click the checkmark beside them, then click the delete button at the top of the list. The books will still be in your purchased books area but will no longer be on your I'm Reading list.
Plug in the reader. Open the desktop software folder and install the software for your type of computer (Windows or Mac). Launch the software, log into your Kobo account. Click the sync button. The books will sync onto the Kobo Reader.
Books loaded onto the reader in this way will not appear as files if you double-click on the device icon in the desktop. If you want them to appear on the device and be editable, you will have to load them through other means