Xj ecu

Here's my dilemma. I purchased a '99 XJ and lagged on getting the jeep registered. I also let the smog expire. When I went in for the required smog just before the registration expired they told me the jeep failed. We determined that since I swapped the battery that I must now drive something like 300-500 miles and hit all sorts of driving perimeters before the ECU trouble restores. My question: is there a way around this?? The smog guy mentioned restoring the computer to its factory settings but for $300. Any ideas? Thank you!!