Did you try reinstalling the software?
do you have some kind of blinking LED in the code to see if program is running?
if not can you add this?

I have had a couple of chips blown (my fault) for different reasons and a couple said they programed and verified but there was no I/O at all, and some just says the programmer cant recognize the chip. as far as programming the old chip with new code and not working but reprogramming with old code does, I'm not sure, is there alot of code changed? is there a OSC setting different? I found I was blowing chips because my programmer software was set to insert the code for telling the chip to use a external crystal, which overode my desire to use interal OSC. chip word turn on and blow because there was no xtal installed. it was a 50/50 result of same issue you have. sometimes it would reprogram and verify but no I/O.