NB: I wish I could claim credit for the following insight, but actually it was emailed to me.
As a matter of style, Moore's works have always tended toward disorganization; as one commentator put it, he wanders about like magpie, picking up anything shiny and sticking it into his nest, wherever it might fit.
But Bowling is exceptional. A film which clearly begins with a theme of firearms, firearm owners, and firearm organizations being dangerous or even evil, ends with a conclusion that having lots of firearms and firearm owners is not a problem after all. We start with the Michigan Militia, and end up talking in his utopia, taking to its resident gunnies about how easy it is to acquire guns.
We don't have a chronology of Bowling, but Moore's statements suggest he began work on Bowling in 2000. He did a lot of the filming over summer, 2001. The K-Mart demonstration occured in June 2001. Moore gave a speech discussing Bowling in July of that year. And the earliest versions of Bowling have a 2001 date assigned, and were showing in February 2002.
It's reasonable to assume that by winter 2001, Moore is well into post production, perhaps ready to put his movie in the can.
Then comes 9/11.
Moore's comment on that shocking event (since deleted from his website, but available elsewhere) began:
This started out as a documentary on gun violence in America, but the largest mass murder in our history was just committed -- without the use of a single gun! Not a single bullet fired! No bomb was set off, no missile was fired, no weapon (i.e., a device that was solely and specifically manufactured to kill humans) was used. A boxcutter! -- I can't stop thinking about this. A thousand gun control laws would not have prevented this massacre. What am I doing?
Might it be that the disjointed nature of Bowling, the complete reversal of its theme in the last ten minutes, stems from this sudden insight? Bowling started out as one movie, but ended as another? (Or at least partially ended as another -- Moore didn't want to have to rework it from the beginning, and so just reshot the end?)