If it's not too much trouble, could you install libgl1-mesa-dev again, run this code and paste the output here?
System.out.println("contextGLFW = " + GLFWLinux.glfwGetGLXContext(window));
System.out.println("contextLWJGL = " + GLX.glXGetCurrentContext());
long glXGetCurrentDisplay = GL.getFunctionProvider().getFunctionAddress("glXGetCurrentDisplay");
if ( glXGetCurrentDisplay != NULL ) {
long displayGLFW = GLFWLinux.glfwGetX11Display();
long displayLWJGL = JNI.callP(glXGetCurrentDisplay);
System.out.println("displayGLFW = " + displayGLFW);
System.out.println("displayLWJGL = " + displayLWJGL);
} else {
System.out.println("glXGetCurrentDisplay not found.");
}
Add it between glfwMakeContextCurrent(window) and GL.createCapabilities(). There is a good chance that simply reinstalling libgl1-mesa-dev won't reproduce the issue. If that happens, try reinstalling the Nvidia drivers, after libgl1-mesa-dev.
edit: Also, see if mesa adds a "libGL.so.1" symlink anywhere.