I agree with PMK, the trike should have had a battery reset when they did the changes and prior to the dyno. And I agree with all of the other steps he outlined....
I also see huge advantages to the way that we flash ECU's and how we are able to basically copy tunes from machine to machine. Why I am getting the one done on the RS-S. I learned from past flash work, they do so much more than the tune, they can correct poorly set rev limiters, and to me the most significant change is this. When the person flashed my Yamaha FZ09 two years ago, he outlined that on stock ECU tunes, hp is actually changed from gear to gear. On production street machines it is not uncommon to restict HP in the top gear for instance. So the FZ09 was rated or ranked at 115 HP stock, in actuality in 6th gear, the motor was only pushing 90 HP in 6th gear or limited to that HP level by each gear basically having its own tune. I was told all imported go through this, and all modern machines with the Keihin type ECU tunes the power ratings to each gear. I asked the people dealing with the monster tunes, and was told this is also the case on the Can Am, and they tune the HP to be the same in each gear which also removes these unspoken governors that exist on our machines. When my FZ09 was flashed, I had 135 HP PER GEAR, and I could lift the front wheel in 6 witht he twist of a wrist even at 80 mph...I sold the bike, it scared me after that, and I had my heart attack on the bike (not speed related).
My other point is I find that Dyno tuning is more of a justifiable expense when you are trying to get the most out of a carbureted machine. Modern ECU based machines such as the Can Am "learn" not only the performance standards, but also "learn" how the rider uses the machines and adjusts the tunes accordingly, in other words if you ride with a hotter hand, you are going to get more performance out of the stock ECU because it has "learned" the speed or performance parameters. SO why dyno tune it unless you are establishing a flash? The need for Dyno tuning honestly went the way of the Carburetor, and good riddance to them both.
With the systems like we have, handle the three basics, Intake, Exhaust, and a good Power Commander (with autotune if you can get it), or Power Vision and you really never have to worry about Dynos or paying for expensive dyno runs that only provide you with data you can get by taking your machine to your local drag strip, and checking it by the seat of your ass. The bike will learn to adapt to the changes once you do a battery reset, and make sure you use the correct maps on your tuner, or set up the autotune.