Searched around, yep, I'm pretty sure the thing is dead now.
I did find this tip which I share here because it was hard to find and topical. Was from a forum on Microchip.
I tried it but it didn't work for me. My signal generator can output up to 20V but I'd noted that there was a high load on the chip, with 3.2V output, connected it dropped to 1V. I'd cranked output on generator to 20V but connected to the chip, it was only about 2.2V ... should be good enough but no, nothing. If it wasn't dead then, it is now.
---
Re: "Unable to enter programming mode" error SAM4S
Thu Feb 18, 2016 7:24 pm
So I have finally figured this bug out.
It turns out in the errata of the SAM3S datasheet, buried deep deep down. (Doc 6500E-ATARM-11-Feb-13, page 1068, (wrongly numbered 11068!).
45.2.4 SAM-BA
45.2.4.1 SAM-BA Boot: Start-up Issue when Using No Clock on XIN
If no crystal (between XIN/XOUT) or no ceramic resonator (between XIN/XOUT) or no bypass mode (on XIN) is used, SAM-BA Boot may not start on some parts. As SAM-BA Boot is running by default when the Flash is erased, the parts cannot be accessed even by JTAG under those conditions.
Problem Fix/Workaround
Use an external crystal or ceramic resonator on XIN/XOUT, or use the Main oscillator in bypass mode (applying a clock on XIN).
My custom made PCB does not have an external clock on XIN/XOUT, I used SCLK (32768 Hz) for timing and the internal oscillator to execute instructions. Consequently, some of my custom PCBs work as SAMBA boots correctly, and some, well, just don't.
So what I did to make these boards work was provide a 1 MHz clock to XIN using a signal generator. Apply power to the PCB, then connect using the ATMEL-Ice. This connects fine. After that I set the GPNVM Bit 1 so we boot from flash, not SAMBA, programmed the device and it works fine.
I sure hope they issue a rev B for this range of chips without this error.
J