Firmata: How can I know if my board is dead?

I have a Duemilanove that has always worked like a charm. In my previous project I used Firmata 2.0 and found it really great. So I decided to use it again, this time I upgraded to Firmata 2.1 so that I could use PDuino. The update went well, I could connect from pduino and get te firmware version, everything seemed to go smooth. But now I cannot update the board anymore. It seems as good as dead.

If I try to upload any other program from the IDE I get the following error:

avrdude: stk500_getsync(): not in sync: resp=0xf9
avrdude: stk500_disable(): protocol error, expect=0x14, resp=0x51

This error is perfectly consistent, every time I try I get the exact same hex codes.

Every now and then the second line says something about the programmer being borked, but I can't reproduce that error message consistently. I tried from both Linux, Windows with the same kind of results.

Is it possible that the Firmata upload has ovewritten some "system" code that might have been there and now I can't program through serial?

Is it possible to "format" the board to clear firmata from it and see if the board is still functional?

I'm a little lost, I do not know how to proceed. Any help is very welcome.

Thanks in advance.