Maybe this is what y'all are looking for?
Note that I've not tried this. I got my phone replaced under warranty a couple of months ago for this problem. It was a bad dock connector in my case. The 'This accessory is not made to work with iPhone' error message started off 'every now and then' and progressed to almost being constant over a period of a couple of months. No amount of restores, cleaning, etc. etc. fixed it.
Also, it's not about just deleting the file. You have to replace the file with a modified version.
Mac Forums - View Single Post - iPhone Dock gives "This accessory is not made to work with iPhone" error
Full version (in Italian, use Google to translate):
.: Suondmao's World - iPhone iapd Reverse Engineering :.
Oh....be sure to back up the original file in case you need to revert back to it!
HTH.