If subfolder/files disappear or are deleted seemingly without any reason, it is most likely done by another folder member. The client itself doesn’t delete anything on his own.
When files are deleted, they aren’t permanently gone but instead moved to an internal file archive first where they can be restored from (look up restoring deleted subfolders or files or Restoring file versions).
When searching for the deleted file in the internal file archive, you can also look up who the last person was to change (delete) the file and figure out why it was deleted in the first place.
As soon as the file is restored the change will be transferred to other clients as well.