So I installed the latest desktop version and synced the ereader with it, downloaded the entire library no dramas. Reboot both PC and Kobo Wifi and connect, the Desktop does a quick sync and all good (doesn't re-download my entire library). So I do it again and same result.
Go to the Kobo Wifi on its own and select "Update Library" and the whole damn library re-downloads again. Argh!!!
Edit: I just did a factory reset and reinstalled the Desktop app. Kobo Wifi still re-downloads the entire library when syncing. Well there goes the option of using the sync functionality