Can you add a "duplicate project with new name"?

Every time I attempt to create a branch of my project (Visual Studio/Visual Micro) the file locations, particularly that of the libraries (user installed) gets screwed up.

At the moment all the #includes in my .ino files are "red underlined" as location missing, although they are all in the c:Ardunio libraries folder, I ca get around the problem by adding the required header files into the file explorer list. 

Can anyone suggest what I have done to prevent, or what I can do to re-enable my User Installed libraries?

Thanks for you help

Tim, Thanks for reply and help.
Before the build I removed all the .h files I had added to the Header Files list in Solution Explorer. Interestingly the red underlining in the .ino file did not reappear. I have sent the build log text file under separate cover as instructed,
Please ignore the reference to .changed in the Bounce library, I have resolved that.
There is still no content listed in the User Installed when I attempt to add a library.
I note your comment regarding "Arduino2", I had noticed this previously and changed it to "Arduino 1.6" etc, setting it back to Arduino2 does caused the red under linings to reappear. Not sure where the Arduino2 entry came from, perhaps it was the default when I loaded the new version of Visual Micro. Perhaps compiling this (somehow) before changing to Arduino1.6 has caused some change in the Add Library User Installed configuration.
Is there a way I can determine/confirm the path of the libraries I have included in my .ino, right hand clicking on the file name does not offer me the "go to location".
Regards
Steve