So far, I have been able to register the Prism v4.1 binaries by changing the aforementioned line from
v4.0 to v5.0 in the RegisterPrismLibrary.proj file with an editor like
NotePad without problems.
If you are using Windows 7, I believe, you could try running the RegisterPrismBinaries.bat file (after changing the aforementioned line) as an administrator, this worked for me in the past.
To do this right Click on the file and select the Run as administrator option.
As an alternative remember that you can always add the reference to the libraries, by browsing the binaries in the
Bin folder where you extracted the Prism source files (to do this go to Add Reference,
Also, regarding the Prism 4.0 folder take into account that for
Silverlight 4 projects you will have to use the Prism 18.104.22.168 binaries. Based on this you will have to decide if you will keep it or not. Also, note that if you have run the
RegisterPrismBinaries.bat from Prism 4.1 without the aforementioned modifications its probably that your past registered binaries for
Silverlight 4 may not work. But if you only run the batch with the modifications then your
Prism 4.0 registered binaries for Silverlight 4 should remain the same.
I hope you find this helpful,