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Did you x-ray the board? Or inspect the inner ball connects with an endoscope camera? I rather expect solder tha device internal shorts.
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Yes, we had several xrays, and they look very clean - no shorts, very concise balls. We actually went a step further and decided to apply a small electric pulse across the shorted IO and ground to see if we could clear the fault. (anything suffering tin whiskers on lead free clears this way).
We place 4VDC, with GND to GND and 4V to the IO pin (which is reverse bias to the protection diodes) briefly across the effected pin. And it cleared the pin and recovered the board! The once dead Ep3C40 passed all its ATE tests.
If it was a PCB failure, i would expect this to be quite explainable, however, the fault definitely manifests itself in the FPGA, as removing the FPGA and replacing it also resolves the problem.
I havent used the endoscope camera as yet, but i did, very gently "rip" the FPGA from a board to inspect the balls - all is very clean, with no white lead free residue under the device - seems perfect.
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