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Firstly of all, the PSoC6 can be programmed using MinProg3 by SWD.
But debug the programming issue, need your schematic about the programming part.
The cypress has offer the new programmer:
Thanks for the response. It turns out that it was a driver issue that presented as PSoC Creator slowing down a lot, and no device target showing up. It was fixed by opening device manager with PSoC Creator opened, uninstalling the MiniProg3 device and others labeled "Unknown devices", then unplugging and re plugging in the USB cable to initiate a reinstall of the MiniProg3 device driver. On some machines, this process had to be repeated a few times. Also, it appears that opening PSoC Programmer and powering the targeted device before this process helped in some instances. Ultimately, the M0 and M4 appeared in the programming window in PSoC Creator, and the device was successfully programmed.