When creating a deployment, the paths do not change. For example, I go to create a deployment of autocad architecture 2013, then I go to the screen where you can customize the file paths. In the search paths and file locations screen I specify a file path for my QNEW template to a certain location.

Once I deploy Autocad Architecture, those file paths that I specified are erased and set back to the default settings. In other words, whatever file paths I customized are gone. Instead of my customized locations, the default locations are instead written in there. See below.