Reproduction steps:

1. Open "CGIncludeBug.zip" project
2. Open "Test" scene
3. See that both Quads are yellow
4. Open the "Include.cginc" file with a text editor
5. Change the "return fixed4(1, 1, 0, 1);" to "return fixed4(0, 1, 0, 1);"
6. Go back to the Editor and see that the right Quad changed to Green, but the left one didn't
7. a) Reimport All (Or just the "SubDirectory" -> "SubDirectory" Shader)
b) 1) Open "SubDirectory" -> "SubDirectory.shader.meta" with a text Editor
2) Do any change and save
3) Go back to the Editor
8. See that the left Quad changed the color to Green

Expected Result: After doing changes to the .cginc file, all relevant shaders should reimport
Actual Result: After doing changes to the .cginc file, only the shader in the same directory reimports

Fixed in: 2018.1.0a3

Reproduced with: 2017.3.0b4, 2017.2.0f3, 2017.1.2f1, 5.6.4f1, 5.5.5f1

Note:
If not Reimported, the shader doesn't change even when making a build