Well, there’s none that exists today. Though it wouldn’t likely take much work to create one.
The key is that if you change the path to your, err, PHP database management script, you’d want to update the config file that Virtualmin has with that info in it.
Virtualmin keeps that information in /etc/webmin/virtual-server/scriptlog/$DOMAIN_ID/*.script.
As long as you keep the Virtualmin config file in sync with the actual path, you should be in good shape and Virtualmin should be able to continue updating your app.
So, just replace all the occurrences of that string within that scriptlog folder (-R), then rename all the directories where the app is installed to match? That doesn’t sound too bad, indeed.
So, I need to loop through the directories in /etc/webmin/virtual-server/scriptlog, identify the files that contain the offending word, and if not in the name= line, replace it with a stealthier folder name.
Since this is probably short work for someone out there, I’ll offer a $20 PayPal bounty, and donate the script back to Virtualmin, if Jamie is interested.