Hi!
Yes, of course, Embedded Wizard Studio is completely independent from the LCD connected with the MCU. If you want to change the LCD of the STM32F429 Discovery Board, you need to change the LTDC timinings and settings according to your LCD. Additionally, the memory area reserved for the framebuffer has to be adapted in order to host the pixel data of the new display.
Within Embedded Wizard Studio, you can set the ScreenSize according to the size of the display - then you can implement your GUI application that fits to the new display.