When making changes to a custom peripheral in XPS, the top level ports and user logic do not change in the project.
XPS makes use of a caching scheme for peripheral netlists.
Therefore, the project will need to be cleaned and re-compiled in order for the changes to take effect.
Follow these steps to apply changes made to custom peripherals:
In order to change the XST Options in XPS, please refer to (Xilinx Answer 52274)