What Ganderite was saying is that every time you cut the barrel you will change it in ways that may well make the load that was accurate at the previous length an inappropriate load for the shorter length. In order to learn anything about whether or not a shorter barrel is more accurate, you would need to develop the best load possible in the shortened one (assuming you have actually already spent the time to develop the best load possible in the barrel before you shorten it). In addition, one five shot group is not really a measure of the accuracy of a barrel at any time. To know anything reliable about the accuracy of a given load in a given barrel you need to test many more rounds. Statistically, a rifle that is really capable of only a 3 inch group may, at any given time, put 5 shots into one inch just by chance.
While the crown of a rifle is often important for accuracy, it is far from the single most important factor in the accuracy a barrel can produce with any given load, so your concern about it may, or may not, be important. You will learn nothing useful about the accuracy of short vs longer barrels from your test. You can get some relevant data about velocity if you shoot enough rounds (I try to use at least 10 rounds for a much better chance of getting a realistic average velocity, extreme spread, and standard deviation, but 5 is way better than one.)
But, as Ganderite said, go ahead. Cut and shoot and let us all know how it goes. Some of us may well be impressed.
