Can you please attach capture of error log and the port setting?
MiniProg3 can work for programming PSoC6.
Please check if there are any voltage limitation circuit on your PCB. Use maximum 3.3V to program PSoC6. Are there any other components sharing the Vtarget from MiniProg3?
If you are using KIT-062, there is a block of over voltage protection circuit. If the voltage of MP3 over the maximum voltage, the supply of PSoC6 will be cut off.
1: make sure the two separate PCBs are been powered.
2: if you use the minprog3 to power your chip, make sure that the voltage is inside the range(1.8-3.6).
3; if you design the power protection like the psoc6 062-kit, sometimes you use the minprog3 3.3v to power it, it also can failed. Because the output may over the tolerance.
4: If you use 2.5v to power it, whether it can be programmed?
I apologize for the late reply, I must have my notifications off.
It happened to be a soldering issue (those darn BGA's can be a pain by hand).
Thank you all for your replies.