I am also having the same problem with Neuro Programmer 3. I last used the software at the very end of April 2018 without a problem but I started to get the .NET framework error when i attempted to open the program again at the very end of May 2018; I opened a ticket with Transparent on June 1. No response then or when I added an addendum to the ticket on June 12 requesting a status update. I suspect that there was a Microsoft Update sometime in May 2018 that broke Neuro Programmer 3 (and other Transparent products from what I gather from posts in this thread).
I checked the registry values for both "HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft.NETFramework" and "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft.NETFramework" and both looked okay. Typically multiple different versions of the .NET framework can be installed side by side on the same machine so I wonder if the version of the .NET framework that the Transparent products were compiled against is now deprecated and was removed by a Microsoft update. That would explain why the required .NET framework cannot be found.
My guess is that a simple recompile of the software against a newer version of the .NET framework would be enough to get everything going again. Maybe a few lines of code might have to be tweaked here or there. If Hewett does not want to do the work himself, you would think it would not be that expensive for him to hire a freelance .NET developer to do the work. Why not preserve the income stream from the Transparent Corp. zombie site and avoid potential legal problems from continuing to knowingly sell broken and defective software? There must be some legal liability for knowingly selling and receiving payment for non-working software and for generally refusing to support previously sold products if those products are still being marketed. I am considering opening a case with the Better Business Bureau.