The Shaders Cleaner for P3D has been updated to version 5a, which now includes the cleaning of the Effects folder as well. It is available for download from the Freeware Section in my Store; and it continues to be downward-compatible with P3D version 3 and 4.
NOTE that after the shaders are cleaned, it may take a little longer for P3D to reload the flight session the next time. The screen may even black out for some seconds. No worry, everything will come back to normal after the shader cache is built again.