I have had problems getting headers referenced in multi-library projects before.
But this time it was weird, in that the Output Error message insisted the Adafruit_ILI9341.h reference to:
was referring to a file that did not exist.
Tried all the usual things - toolchain referencing & project build order, but nothing.
In the end I copied the Adafruit_GFX.h into the folder of the application project and the solution built fine.
Maybe not surprising, but then I deleted the header and the solution still built.
So now it's fixed, but am not sure what happened; either why the error ocurred in the first place, or especially why it went away.