On the face of it the changes you state that you have made shouldn't stop the FPP functionality working. Just to confirm - you haven't changed the pinout or rtl from one design to the next?
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When i program it by using Quartus-II PC programmer
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By 'it' I assume you're referring to configuration of the FPGA? Can you confirm that you can successfully configure the CPLD?
Assuming you have not changed anything else, have you confirmed you can use your previous design with Quartus v13.1? Have you tried a previous release (try 12.1sp1) on your new hardware?
Final thought, the FLASH loader IP isn't something you're missing license for, is it? Is Quartus v13.1 pointing at an appropriate license?