Since posting this question we have found the following fix:
After importing the x64 registry settings, the NPrinting designer now works correctly again.
We are thinking that in the process of uninstalling Office 2013 and installing Office 2016, the referenced registry keys were broken by the installer.
I gave this a try and I still receive the following when trying to run a report:
Message Date Time Error Error: QlikView NPrinting can't find a supported reporting output producer for the file C:\Users\grant.smith\Desktop\EZView\Production HRM Reports Template CDM Baseline Only.pptx. 11/4/2016 12:38:19 PM
Does the NP works fine with creating new excel templates and also editing an existing template?
I ran the fix and then the creating new template worked fine, but when trying to edit it I ran into the same error message again..
I manually checked all the reg keys and they are all set to 16..
I also restarted the machine and everything..