Removing installed script without uninstalling it

It often happens that customers install a script, then just delete the contents from public_html/ and replace it with something else.
However, an entry for their script (of course) remains in Virtualmin, which makes it possible to upgrade, which could replace files of the current application, or uninstall, which would delete the application.
So how can I just tell Virtualmin that that script is no longer installed?