To reproduce:
1. Open attached project;
2. In the project tab, select shaders/Material1 so that it appears in the Inspector on the right. You should see a red sphere in the preview.
3. Open the file Assets\shaders\subdir\blah.cginc
4. Change the green value so that it reads "half GreenValue() { return 1; }"
5. Check the Sphere.

Expected result: The shader immediately updates with the new color.
Actual result: The Sphere stays with the same color.

Reproduced in: 5.4.4p4; 5.5.0f3; 5.5.2p1; 5.6.0b10; 2017.1.0a2

Note: If you change values in Test1.shader , sphere color changes immediately.