If he still has the leather Pak then it's a CVO, if he threw it away he may get some arguments. Bottom line: he didn't destroy anything intrinsically CVO, he only added something. If you repaint, that's another story and not comparable. Although the bike may be more functional and weather resistant, I seriously doubt he increased the resale value.
He didn't actually throw it away,he was able to trade it on the new TP with the dealer. So essentially he made a major change to the stock CVO for his own personal use such as changing the paint scheme.
As mentioned prior, I feel if you when you have a bike you might as well get as much enjoyment out of it as possible and paint it, add/subtract/change parts do whatever you like 'cause it's YOURS and don't think about the resale value... As someone else mentioned you may make a change that your purchaser may really likes and therefore your change has increased the value - to that buyer.
As for buying new tins to paint and keeping the original for resale purposes... For the amount of money you will pay for the extra tins, I don't feel you will ever make up that money on resale. I remember when I was custom painting my '91 Heritage and I wanted a 5 gallon tank installed at the same time. My dealer convinced me not to break up the set and to purchase new fenders as well, that way I could sell the originals as a set. I took his advise and attempted to sell the set of tins, which at the time was the most popular colour (2-Tone Ruby) in the Harley line up. They now hang on my garage wall!
The upside is that I love my custom painted Heritage and have had years of enjoyment turning heads while riding it.