Deleting a user account or a project results in Uploads folder being deleted.
We have BugNet Version 1.6.329.0 with few projects where attachments are stored in file system for all of them. I created a new user and spelled the login name wrong so decided to delete it straightaway. Deleting that user also deleted the Uploads folder with all its content. I later tested it with projects - creating a new project and immediately deleting it - Uploads folder was also deleted.
I don't see any sort of cascade delete setup for users but I will try it and see. It is by design that when deleting a project is also deletes the attachments but it would only delete the project folder itself not the whole uploads folder.
If it is of any help, the DB and the Uploads folder were migrated through a good few versions of bugnet over recent years, starting at 0.8 if I'm not mistaken. It was always an updrade, never a clean installation. Not sure how the web.config file was updated, but I guess it was done as prescribed in the manual/forum.