I’m using 32 GB cards with no problems. I don’t know if I’ve seen anybody use larger.
My first step would be to try the card in a computer or other device. If it’s recognized, try formatting it there. Also, see if you can actually copy 64 GB onto the card and still properly read things back (there are a distressing number of fake large capacity cards that are really much smaller, but that doesn’t show up until you use up the actual capacity of the card or try to format it.)
Any existing format on the card shouldn’t really matter: pretty much the first thing that the disk expander sketch does is partition and reformat the SD card.
Remove SD from Yun. Power up. Login or use YunSerialTerminal to get to the command line on the Linux side of the Yun.
Then at the command line run
ls -l /dev/
now repeat #1 & #2, except plugin the SD card.
I would add a step between 2 and 3: after capturing the information from step 2, insert the SD card and repeat the dmesg command: there should be some new messages at the end showing the attempt to mount the SD card. They could be interesting to see. Then, with the SD card in, repeat steps 1 and 2 (cycle power and capture output) so Jesse can compare the two boot sequences.