It is true that engines that are brand will get broken in, increasing their power slightly, then will start to decrease over time. Oil changes and engine overhauls will help with keeping your engine well maintained, but there will come a time when permanent power loss will come into effect. But it will be a very long time though.
Also, if you complete the race regardless of, well, anything except for disqualifications due to race conditions i.e. going of track and you're not supposed to (not the case here though), you are supposed to receive any prize money and experience from that race. The only time the PP limit regulation failure comes into play is when you are entering the race, but the game doesn't allow you to. I had the same thing happen to me on the same event, but I still got my cash and exp. Just lower the power using the power limiter each time by about 3 or 4 PP (yes PP) when it is close to the limit.
Well, just be glad it was only 3 minutes instead of 24 hours, even though there's no PP limit in the endurance races. Now that would really suck.