This issue had been discussed on support forums: https://www.virtualmin.com/node/21810 but never was filed as an issue.
If you delete FTP users then directories associated with those FTP users get also deleted. One of our customers did so and because we had to restore his website from the last backup he lost lots of data entered since the date of last backup.
The files and directories of the documents roots should always be independent of any additional FTP users. Virtualmin admins can create lots of temporary FTP users with access to various parts of websites, but when times come to remove those FTP users, they should not deal with this dependency issue.
I believe this is critical issue that needs to be addressed ASAP.