The files and folders are displayed by DNN based on what has been captured, and synced by DNN into its tables.

1) Go to Host->File Manager ---- (This is where you host files are managed by dnn)
2) Check the check box on top right had corner inside the File Manager that says "Recursive"
3) Hit "Sync" button inside File Manager

Now,

1) Go to Admin->File Manager --- (This is where your portal files are managed by DNN)
2) Check the check box on top right had corner inside the File Manager that says "Recursive"
3) Hit "Sync" button inside File Manager

Next, you need to delete the cache as all the above is usually held in cache. So go to "Host->Host Settings" and under "performance" hit "Delete Cache". Logout and close that instance of the browser. Open a new instance and do your thing. If the file sync was successfull then you should now see all your folders. Remember you need to put all your folders INSIDE "Portals/<<Portal Number>>/" path, else your store won't be able to show them. Store works under a specific portal and hence its image folder need to exist within that portal folder. It cannot access other portals folders - good security I say.

Hope above helps,

Sincerely,