Yes to both questions. I always stop the device before removing the storage device. Some files are visibile on the sewing machine and others are not. I read in the manual that I should not be creating folders because the sewing files in them wouldn't appear on the machine, but even that isn't consistent. When I have the embroidery unit attached, I can see files both inside subfolders and the ones that are in the higher level folder when I click to open the folders. When I don't have the unit attached, all that I can see if the folders and I can see nothing in them.
This is my second Ellageo. On the old one, I had the same issue occasionally when reading from "floppies" but I did something - I don't remember what - to get around it.
Thanks!