Because Swarm is not a traditional file system, you may need to change how you have historically used placeholder files and folders using dummy 0-byte files.
Folders — Note that client-side folders are not the equivalent of Swarm or S3 buckets. The folders you create on the client side are handled as pseudo folders that are incorporated into the object name in Swarm (psuedo-folder1/psuedo-folder2/filename.ext), which are expressed as folders when translated back to the client side. If there are no content objects to be uploaded to Swarm needing the pseudo folder, it will have no reason to exist in Swarm.
Files — The only 0-byte content objects native to Swarm are special metadata-only objects used for object annotation. If a client-side object has no content (0 bytes), FileFly will not recognize that there is anything needing to be stubbed and sent to Swarm. Therefore, when you do a DrTool recovery, those placeholder files will not be restored, because they never existed in Swarm.