Solved. Converted everything from Mobi to AZW3 deleted all the mobis off the pw and resent the AZW3s - the metadata transferred fine and I did the collections on the device. SUPER annoying because as soon as you create a collection you get a warning that it's not gonna sync cuz the wifi is off then every single book you tick to add to the new collection you get an error message about it not syncing. EVERY. SINGLE. BOOK.
But whatever I got it done - though the covers did disappear once in collections I changed it to list view and forgot about it
Hope this helps someone else so they don't have to waste all those hours like i did!