I think there is a limit to the number of files you can copy to the root. You can only have so many that are not in folders
Try this and see if it works
Make some folders on your desktop name them what you want. E.g. “Pictures 1”, “Pictures 2” etc
Then "move" or "cut" not copy
all the photos from the card into the folders on the desktop.
Once all the photos are in the folders on the desktop, cut the folders off the desktop and paste back onto the card.
Files in a folder count as 1 file in the Root directory even if it has many files.