Since your project is working on the development kit but not working on your board, we are suspecting that there might be an issue with the schematic. Please attach the schematic to check. Or if you dont want to share, please compare it with CY8C4014FNI-421AT kit's schematic.
If schematic is fine and the issue is there, please program a simple blinky project and see if the device operation retains over the power cycle.
In case the blinky project also wont work after the power cycle, please send us a video showing how you are actually programming and testing.
Below provided is the PSoC 4 schematic. Kindly review and let me know about any further concerns.
(1) As PSoC 4 WLCSP (CY8C4014FNI-421AT) device which doesn't have an external reset pin (XRES), I am shorting all the 3.3 V pins together (VCC_PSoC) and isolated it from 1.8 V (VCCD) via voltage regulator so that while using MiniProg3 in Powercycle mode, I can power down and switch on the entire device uniformly in a way similar to the Reset programming mode.
(2) I am shorting pins A3 to B3 and C3 with C4 pins due to manufacturing difficulties in accessing required pins.
With PSoC Vddd at 3.3V, there should be no other connection to Vccd pin except a 0.1uF capacitor. See datasheet, Power chapter.
1) Remove the 1.8V regulator connection to PSoC 4014 Vccd pin.
2) Ensure the 0.1uF capacitor is still connected to Vccd pin.
And now you should have a working solution with Miniprog3.
When powering PSoC 4014 with Vddd at 1.8V, you can (it's an option) connect Vccd to the 1.8V regulator. It's also recommended to disable the internal PSoC 1.8V regulator as detailed in datasheet Power chapter when PSoC 4014 is powered with Vddd at 1.8V.
Let us know how it works out.
Good luck with your project.
Thank you very much. The workaround you suggested helped resolve the issue.