Hello,
I had the same problem when making the backup, it would be interesting to add these notes in:
https://retropie.org.uk/docs/Updating-RetroPie/#making-a-backup
Change "Make sure you have the correct drive letter for your SD card!" to "Make sure you have the correct drive letter for your SD card! (Choose the partition which is readable by Windows, 'boot' as the source of the backup)" or something similar.
Thank you.