Please see the most recent updates in the "Where did the .com name go?" thread. Posts number 16 and 17.
Ah no, the sim will not rebuild the shaders. It will only rebuild the shader compilated files which are in c:\users\...\appdata\local\...
It won't rebuild the files in P3Dv4\ShaderHSLS\.
If PTA doesn't include an option to restore the shaders, then you could simply uninstall and reinstall the "client" part of P3D.