Removing Install Script Control of Directories / Databases

In short, I have a Drupal Install Script install that I'd like to take from out of under Virtualmin control.

Is that as simple as removing the file related to the install in /etc/webmin/virtual-server/scriptlog/nnnnn/xxxxxx.script?

The longer explanation --

A user installed version N of Drupal via the Install Scripts. They wanted a more recent version though, and upgraded it manually from a package on the Drupal website.

Attempting to modify their install using the Install Scripts would almost most certainly break it now, I'd imagine (or even if not, they like the version they have :-)

Thanks!