I assume you have a B9 2016/17 model?
I've got a 128gb card in mine and whilst it see's it , for some reason it isn't picking up a lot of the music on there (my Seat Cupra 2014 model saw everything fine).
Are you seeing everything you should do on your 64gb card?
Can't seem to find anyone having the same issues (to be fair there seems to be a lot less people on forums for audi than there are on Seat cupra forums... so its hard to find out anything)
I formatted it as FAT32. I've done a bit of reading around and it appears as though there is a maximum number of files that can be read on the card. Another post seemed to think it was around 10,000 files, irrespective of how big your SD Card is. Seems a bit of a limitation, but it would explain my issue as I have 17k files on my card