Just for fun!
You're trying to shoot a cleric, who has just cast a spell, laughed an evil laugh, and cried, "I have put up an /antimagic field/! Nothing can stop me now!" You're not sure whether to believe her.
Between you and the cleric, there's a giant you don't like. He's 15' away from the cleric---definitely not in the /antimagic field/, if it exists. He's also big enough to give the cleric 1/4 cover. You don't mind shooting him, but you'd rather hit the cleric.
You have either a +3 bow and two normal arrows or a normal bow and two +3 arrows. One of the two arrows is poisoned. Naturally, this is the arrow you fire first.
You have a BAB of +10, a 14 Dex, and no other modifiers to your attack roll.
The cleric has AC 23, but the cover increases this to 25. The giant has AC 15.
Your iterative archery attack rolls are 10 and 14.
If your weapon enhancement ignores antimagic, then this is no problem. The poisoned arrow hits AC 25 and hits your target. The second arrow hits AC 24 and hits the giant.
Suppose that an antimagic field, if it exists, would invalidate your weapon's magic.
Does it matter to the giant?
The problem is: if your weapon enhancement goes away, leaving only a masterwork bonus, then these shots miss by 2 and 3, respectively. The giant is suddenly hit by the poisoned arrow and missed by the regular arrow---even though the arrows never entered the /antimagic field/. Why did the first arrow hit? Why did the second arrow miss?
If you rule that the poisoned arrow misses the giant, then you have an oddity: you missed the cleric only because the cover was there, but you didn't actually hit the cover. Does the arrow go around the giant?
If you rule that both arrows hit the giant, then you have another oddity: the giant's only providing 1/4 cover, but gets hit 20% of the time. (When you roll to hit AC 21-24.) The /antimagic field/ behind him makes him a very big target.
If you house rule that the enhancement bonus applies regardless of the /field/, then you have oddities involving whips and polearms of really large monsters. (You can't entirely ignore the fourth oddity, since some creatures might have a rakshasa-like instant-death vulnerability to being struck with the haft of a weapon. Some, er, very odd creatures.)
You could rule that the enhancement bonus helps overcome cover that's outside the field. This is actually a pretty good ruling for you, but it's absurdly good for the giant---he can stand right in the arrow lane and never get hit. It would strongly suggest that magic remains with the arrow all the way to the target, at the very least---since you care an awful lot about whether the cleric cast /antimagic field/ or a Widened /antimagic field/ with a 15' radius.
Rebecca