Thank you for the post.
I am not able to replicate by stopping and starting progressive backups.
How were the folders initially created? Was FileMaker Pro 13 used to upload the files and create the folders?
Did anything change about the folders or directory structure? Were files moved manually? Were any folders deleted after backups completed?
Anything else that may help me replicate?
I have resolved the deleted subfolder in the progressive backup folder by unchecking the progressive backup option, moving the existing subfolders under the progressive backup folder to a different folder, and re-enabling the progressive backups.
This problem is now resolved.