Cyclone IV GX dev kit HSMC connection buned MAXII BGA chip

This is probably not an explanation why the MAX II smoked, but I just want to point out one thing:

By default the C4GX Dev Kit is configured to use 1.8V as the I/O voltage for banks 5 & 6. And many of the HSMC pins are connected to banks 5 & 6 ...

In order to change to IO voltage 2.5V for those banks, you should shunt the jumper J3. See the table 2-45 in the G4GX DevKit reference manual.

We were lucky and our board survived but without this jumper our HSMC board did not work correctly ...

Regards,

Jari