Hopefully you are using a CY8CKIT-050 with a PSoC5 LP chip. The older one (without "LP") are not supported any longer.
Programming and debugging usually runs flawlessly. I would suggest you to check/change the USB cable between J1 and your PC.
I have no doubt about cable. I also checked the schematic of the kit. There is a Component U3 which is EEPROM flash, why it is used in kit with U5.
EEProm contains the programming of the USB interface chip. There have been issues with the cable some years ago.
Creaate a support case!