USB Flash Drive are convenient, but in my experience, its not ideal to store collections of small files & deep nested directories, especially if formatted with the ExFat filesystem. I format most of my external drives as ExFat as this helps me read them on Debian Linux & MS Windows 11. USB Flash Drives formatted with ExFat work really well large single files. However, in my experience when transferring a collection of smaller files, transfers are slow & unreliable. Forgetting this & starting a file transfer can make you end up losing valuable time or data.

I recommend backing up directories to ExFat filesystem by grouping the files in a single uncompressed archive & then transferring this archive to the flash drive. Archives can be transferred between filesystems easily.