I was under a spam attack with over 100K fake users, had to disable registration, in the process of deleting all users as per Sebastian Leupold blog article:

http://www.dnnsoftware.com/community-blog/cid/155027/quick-tip-getting-rid-of-spam-users

Deleted all users folders manually, from the server via remote desktop access.

I then went to the File Manager/Admin  to  perform a sync to get rid of all folder entries and folder permissions in the database.

With over 100K user folders, it is taking sometime, with 12 hours now and I am half way thought, while with little impact on site performance

Have noticed the folders reference is being removed without an issue (table: "folders") but the corresponding folder permissions (in table: folderpermisssions) are NOT REMOVED!

With an average of 5 rows in the permissions table per folder, I'm having over 500,000 Orphan rows in the folderpemissions table .

I am using DNN 7.3.4, SQL 2012 web edition on a Win 2102 standard edition.

Thanks alot, Sebastian!

I was about to post an identical workaround (see below script). As for the foreign key insertion, I rather wait for your script, than me messing around with the folders and folderpermission tables  :)

I run the below script on a development portal with a clone copy of the database via the SQL/Host and SQL Management Studio, both worked seamlessly.

BTW, I also tested the delete folder function in the File Management/ADMIN, and still the issue of not removing the folder permissions are there, it seems a bug in the Folder Sync function of DNN. 

FYI: successfully executing the script took max 10 mins while the folder sync a whole day !

use [NAMEOFYOURDATABASE]
DELETE FROM FolderPermission 
WHERE FolderID NOT IN (SELECT FolderID FROM Folders)