Programmatically configure HotFolders

System

We are in a situation where we would like to programmatically configure HotFolders and also address the silly password connected to a user issue.

I noticed that all the HotFolder configurations seemed to be stored in the HotFolder config .xml file. Can I programmatically stop the mbpublication service, alter the xml in the configuration, and start the mbpublication service?

Are there any gotchas to watch out for?