Hi, I had a similar problem on the STM746 Discovery board. What I remember is that the was that the images in external flash needed to be re-programmed every time they you change them (Usinf the st-flash tool and setting up its driver to access the external flash. Driver was built into the tool you just had to select the correct one). Development environments generally only know about the processor and its internal flash. External flashes mostly have to be programmed separately
Can't remember the exact details but there was a tutorial on ToughGFX website.
I remember my work flow was something like this:
Create project with initial screen layout etc as you have done
Generate the binary
Use st-flash tool to program the binary
Then start debugging (if the touch GFX part stays constant then reprogramming external flash was not necessary )
If GUI changes then external flash need s to be reporogrammed.
Hope This helps