Having a quick look, it seems that GPIO handling part should be changed as per your board design.
1.I have arranged the Hardware as per Evaluation Board
2.I have taken MSC_EEPROM_scan_LCP_v2.bin file from ..AN15484\Memory Stick Code CY4640\sbc\msc_api..location
3.I have uploaded using EEPROM Programmer and and connected SCL and SDA lines to cypress
4.According to program whenever pendrive is connected/removed from USB. A interrupt pulse should generated to GPIO25 pin.
5.But I didnt find any pulse from GPIO25 pin Observed with CRO.
Please guide me what will causes..Accroding to that I will check
Thanks and Regards