Chances are the dealer wont touch it. According to Chrysler and ecudirect, once an ECM is burned to a vin, thats it, it cannot be burned to another vin, the skim cannot be removed. Only software updates available for whatever vin is in the ecm can be done. The local dealer here laughed when I took the first one to them to have it flashed. They said the entire swap was not possible, and the engine would never run. Its been running on the 2.7 electronics ever since.
ECU's can be swapped, problem is, the anti-theft is non-removable (so says ecudirect.com) so if you have a SKIM ecu, you are screwed--unless you have the key ring and BCM from the donor car to go with it.
Best thing to do is use the 2.7 electronics. If not, you will have to find a vin from a non-skim car, with a 3.2, and have an ecm burned to it-- or find a car with a used ECM--without skim.
I have such a vin, I just went thru this myself. My 2.7 ecu went bad after running fine for 2 years. I dont have the new ecu yet, should be here later this week. Its for a 1998 3.2L car without skim. To find it I simply searched for 98 Intrepid ES on auto trader. You can call the parts department at the Chrysler dealer with the vin and they can tell you if the ECU has anti-theft or not.
Not true on the VIN change. It can be done very easily provided you have the PIN for the vehicle you are putting it in (or the PIN from the non-SKIM donor car).
It is a simple proceedure, done it several times.
As far as the anti-theft, I haven't been able to disable it - (yet, as it receives the SKIM info and keeps it in it's internal memory. If that could be erased, then the ECM would work in non-SKIM cars)- but all that is needed is the SKIM and key that matches the engine controller, not the BCM, it is just a message-relay, doesn't actually have a bearing on the anti-theft.
As far as reflashing the engine controllers is concerned, you can only reflash to a "better" setting - the 2.7 can be reset to a 3.2/5, but not the other way around, or a 3.5 from the ES could be reflashed to a 300M (higher HP settings), but not the other way.
I thought we had discussed all this when I was at your place.