Please use PDL version 3.0.1 only ,PDL ver 3.1.0 is not compatible with PSoC6 rev*A.
Open PSoC Programmer 3.28 and do Erase All.
Then try to debug.
If possible please get a replacement for rev*A PSoC6.
I got same issue with rev*B PSoC6 on CY8CKIT-062, then when I did erase all using PP3.28 and Cyprogrammer available at these link, I was able to debug in PSoC Creator4.2:
Works like a champ! Thank you very much.