If it got too hot to touch, the likelyhood is that the FPGA is now an ex-FPGA, having gone to join the choir invisible. One possible cause is that it latched-up into a high-current mode (a more or less common problem with CMOS architectures under the right conditions) and this has toasted the I/O drivers. Did you manage to program a pin as an output and drive it with another output? That can sometimes do it.

It's certainly not impossible to program a device in a way that causes a thermal mismanagement error (TME ). I designed a board many years ago that used a Motorola DSP56001 processor, in a PGA ceramic package. The things were not all that cheap, but very fast for the time, and fairly low-power. The programmer and I were debugging the board one day when the test program we had just loaded stopped responding, and while we were poking around trying to figure out what was wrong we became aware of a 'hot' smell, like a clean frying pan on a hotplate.

The programmer, not being quite as paranoid in such situations as I am, reached over and rather incautiously placed a finger on the DSP. There was a brief sizzling noise, a somewhat more prolonged howling noise, and he ended up with 'OTORL' branded backwards across a now-shiny fingertip.

It turned out that there was a bug in that iteration of the processor, which allowed you to program it into a self-destruct mode where it suddenly began emulating a heating element. We blew up a couple more in the same way before we found out how to avoid it.

Replace the FPGA, find out what the maximum current it should ever take in normal circumstances is, and put a fuse of just over that value in the power feed to the board.

pca
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Experience is what you get just after it would have helped...