I found the reference to the Lincoln being armed - it was in Tony Geraghty's history of Brixmis. The Brixmis team that went out to the crash site was, apparently, convinced that the guns were loaded, and that the BOI report (which blamed the navigator for getting lost) was inaccurate. Subtext being that the affil ex was just a cover.
This, of course, doesn't mean that the Brixmis team got it right (for instance, the Russians might have been tempted to doctor the crash site by introducing 20mm ammo to the scene... - 'We are very sorry, comrade, but you will understand that once the aircraft fired at our fighter...') - but it is an interesting little tale...