There is following setting that you should try: Open the default music player app (green triangle symbol), select the settings menu here (three dots under the clock top right). Here select "settings". You will see options for HD Library Sync, by default it is set to Automatic. You can start sync manually, or select / deselect folders for syncing.
Also, I have uploaded the Onkyo Manual here, not sure how many downloads wetransfer will allow before closing the link in a week or so... Unfortunately I have no authorisation to attach docs here, does anyone know how to get this?
https://www.wetransfer.com/downloads/ccda20f391e1221a57331b75842b0d3c20151219075259/aaffa82991fc6591a755a733c4526b8320151219075259/62ba6e
One more learning point for fellow users: When listening to high resolution files, don't use the Lock Range Adjustment's most narrow setting, otherwise you will hear irregular interruptions / blips when listening. I went though hours of reformatting / swapping sd cards and so on, after I realised that the issue was that setting..