I owe you all an update. After much consideration, I decided I wanted to keep the guitar. I did a little research on the store and this salesperson, I found perhaps 3 so so reviews out of 50 high reviews and those bad ones were minor. The salesperson I was doing business with was highly praised and has been there a long time (store has been in business for 40 years).
I decided to let the salesperson address his side after he researched what happen. First, he told me he did not want me to have this guitar if for any reason I felt it would be tainted. He wanted me happy and offered all three options I listed on his own....+1. He explained he did not know the history and apologize for this. The salesperson that had sold it is no longer with the store (fired before this all happened). He was selling gear at or slightly above cost to boost his sales volume, this was not store policy. I imagine those lucky few customers are very happy!
The timing of the first sale was at the time folks received the stimulus money. I imagine he purchased this hoping to hide it from his wife, it did not end well for him! (Totally speculation on my part).
Back to the salesperson:
He offered the guitar at a very good price with a direct refund and not a store credit. another +1.
He offered a full refund..+1
He offered to order a new CE24 at the very good price. But, he had contacted the factory that morning to see if he could get one off the assembly line and the best that can be done would take up to 8 months. This was a honesty checkpoint for me. I emailed PRS with their lead-time for a new CE24 Amber the day all this happened. They responded almost immediately and said the lead-time is 6 to 8 months...+1
I also asked the PRS CS if they considered this a new guitar. They were very PC....if their dealer considers this a new guitar sale, they do too and fully honor the warranty.
The salesperson restored his integrity in my mind. As pointed out in several comments, if I had not seen that receipt, I would have been happy with the original deal. The new deal was too good to pass up. I was able to purchase the Mannmade bridge and a practice amp from the refund deal he made me. We both agreed we wished that receipt had never been found.
The volume control was not loose as I and he had thought. The shaft has a lot of play in it, to the point it feels like a loose pot. The CE model has the American made pick-ups and jack, but the electronic (volume, tone, switch) are sourced from a different manufacture than what is used in the Core Custom 24. according the PRS CS. I spoke to Dave Mann, he thought they were the same, but in any case, he provides the same components as the Core, so I might change them out eventually.
Bottom line, I am a proud owner of a "new" CE24 Amber that plays great, which I got it for a fantastic price. I am happy. As far as dealing with the store in the future, I don't know. They are the type of music store that is getting harder to find, one that I have always been comfortable in, so most likely I will.
I want to thank all that responded. I appreciate all the comments, they helped solidify my decision.