I have a hard time believing that the museum would be stupid enough to intentionally remove American flags, but then maybe I'm underestimating the idiocy of French anti-Americanism. If that turns out to be true and it got out in the American mainstream media the French could pretty much kiss off any return of American tourists or purchases of French wine.
The French always seem to be worried about the Arab street but they are finding out the hard way that pissing off the American street carries a lot more consequences.