Can i use Mini Prog3 to program BLE chip?
SCNR. I'm engineer, and you asked a yes-no question :)
When you look at the BLE board, you see the 5 pins that are dedicated for programming (called 'prog'). Connected to Miniprog3 there - you will need a adapter for the connector there.
To extend that: the SWD pins of the PSoC5LP are normal GPIOs, so they cannot handle voltages higher than their Vddio. I'm not sure whether KitProg can reduce its output voltage - if not, the target board should not be powered with less that 5V during programming.