Burned Arduino?

Hello dear Arduino users.
AS i mention in the topic,i experimented with my Arduino duemilanove on analog read function.I wired my pot from ground and +12v,and the input to Analog 5(so 12v got into analog pin).I use 12 volts usually from the battery,and because arduino has it's own regulator was never a problem.Now i try in the arduino IDE to reprogram it but gave me some errors.I also have the AVR DRagon connected to ISP but i cant read any signatures.
The error in IDE say something like this:

avrdude: stk500_getsync(): not in sync: resp=0x00
avrdude: stk500_disable(): protocol error, expect=0x14, resp=0x51

The strange part is that the code programmed inside is still working,but with no way to communicate with the board.Should i try HV erase the microcontroller?
I mention that i saw a flicker to the "L" led on the arduino board when the 12V got into it,but dnow what that means.
Any ideas are greatly apreciated.Thank you.

I use 12 volts usually from the battery,and because arduino has it's own regulator was never a problem.

This part is a little bit confusing. I think you meant to say putting 12V into the Arduino (either the barrel jack or Vin Pin) never had an issue because of the on-board regulator. However, in this case you put 12V into Analog In by mistake. Which has nothing to do with the regulator.

The Max input to any of the Arduino's inputs is ~5V. It is possible you destroyed the ATmega but it isn't likely. Usually you will just loose the I/O pin.

When trying to upload do any of the lights near the USB port flash at all? Maybe there was another mistake in your wiring that damaged the FT232 chip. Does it (or the Arduino) get warm/hot after being on for a few minutes?

If the FT232 is getting warm then it isn't the ATmega. If you can find one in stock or have another microprocessor handy, you can try swapping it out to see if communication resumes.

You might also try manually resetting the board just before uploading to see if the auto-reset is broken. (Search for your error message, there are about 6,000 pages on google that give this and other troubleshooting steps.)

Thanks for the Tips.If i take down the atmega,i can hear the sound when plug in the usb into the board(driver ok i think),but when i try to upload,only the Rx led flashes.Tx is doing nothing.Meither of the 2 chips get hot,the board is like in the normal state.
Is there a way to burn in the boatloader with AVR Studio?I have the AVR Dragon around for ISP communication.Thanks

Your Arduino duemilanove has a FTDI chip that converts USB to serial. It sounds like your excess voltage leaked from the pin to the supply rails and killed this chip. This is responsible for communicating with the PC and doing data transfer. It is likely that your ATMEGA chip is damaged but still managing to function although it's long term life time might have been shortened.
You need to replace the FTDI chip but sadly these are surface mount and not easy to replace.