What is the best way to update the BKS?
The core classes are the simplest, they were designed so that any changes you need to make can be done by subclassing. You can just replace the BKeeney_Shorts Folder outright.
If you've made any customizations to the inner workings of the visual report designer you'll need to know where they are and what you did. Any of the support advice provided through Mantis is already included, and you don't need to worry about those changes.