I tried rclone rmdirs --leave-root "ftpserver:Test Folder"
at the end of the loop but that didn't seem to work.
However, the below looks like it's working after a few tests. I'll continue to test some more and fingers crossed this seems to be the one.
while read -r folder; do
rm -rf "/mnt/user/Media/Test Folder/${folder}"
rclone move "ftpserver:Test Folder/${folder}" "/mnt/user/Media/Test Folder/${folder}" --progress --transfers=1 -vv
rclone rmdirs "ftpserver:Test Folder/${folder}"
done < <(rclone lsf --dirs-only "ftpserver:Test Folder")
Thanks so much for your help. I tried to find another way to change the for loop before you suggested the while read loop but never came across the while read loop.