according to official H-D standards, frames can not be realigned nor welded but have to be replaced. So your only choice will be to just ignore the frame or have the bike reassembled with a new frame.
I had the situation 2003 when a car decided to change lanes in front of me without consulting his mirror. Engine guard was pretty folded and damage to the frame most likely if not evident. But as we were booked on a tour to Russia just 5 days later I decided to ignore after meticulous test ride. Had the bike for 2 more years and some 40.000 m, never realised any change in ride characteristics. But was carefull enough to sell the bike to the dealer who seconded the decision not to measure the frame

On the other hand a friend last autumn got victimized by his clutch just the day after delivery of his red FLHTCUSE4. Ran against his garage-door. Fairing, engine guard, mirrors damaged - and frame. It took 6 weeks to get the parts together, dealer let him ride the bike on his own responsibility (he avoided higher speeds, didn't realise any change in handling though), bike was rebuilt in another 4 days and I believe he got a better quality now than out of the factory: each screw was torqued to the book, many little issues manually realigned ...
But we do have an outstanding workshop over here. As our dealer trades in Ferrari, Maserati, Aston-Martin and Rolls-Royce too, they have all imagineable tools and a top quality workforce with experts in any field.
If you can't trust your dealer to get the job done properly I would seriously consider to ignore the frame. But you will have a problem selling the bike so trading her in now as she is might even be the best choice for you ...