When only the UCF file is modified in the EDK project, the "Export to SDK" function updates the new bit file in the "SDK\SDK_Export" directory. However, the bit file in "SDK\SDK_Workspace_35\hw_platform_0" is not updated. Since "SDK\SDK_Workspace_35\hw_platform_0" is the default directory that "Program FPGA" takes, the FPGA function did not change if you program FPGA within SDK after the export.