To me it seems preety cut and dry.
Defending lets you TRANSFER these bonuses from the "enhancement" department to the "special AC" department.
In the enhancement department, the bonuses are hard at work, making sure your weapon can hit easier, deal more damage, penetrate that DR, and take the abuse of other magical weapons.
But it tuesday, and the bonuses are moving to a new department. They now work tirelessly, making sure there weilder doesn't get harmed by all sorts of attacks. But as efficient as they are, they can't work in two departments.
So now the enhancement department is understaffed (in fact no one is working), so no easier hitting, no more damage, just nothing doing.
The boss gets a little tired of this, thinking while the new bonuses are nice, he'd like to have some hitters in his enhancement department. But wait he thinks, the B team!!
Those adamantite boys from the southern department have been sitting on their butts for too long. Sure they've always been good workers, except in the damage reduction sector, never too good with the paperwork, but always crackin with the extra hitting and damage dealing. the boss had been wanting to bring them in, but the enhancement department can only handle so many, so they've been on the sidelines.
But hey, now that the old squad was transfered, perhaps its time to bring in these other guys and let them have a go.
Personally, part of this is crystal clear. +2 defending adamantite longsword can transfer +1 to the AC, and will still have the adamantite's bonus (which being +2, will overlap with the +1 magical bonus, leaving a +2 bonus). It won't help against DR, but for everything else it works just fine. I haven't seen a good argument to counter this.
Now the things that are tricky.
Can you transfer all of the magical bonus? According to the defending description you can, but as others have said that would take out the special enhancements including defending. I propose three alternate ways of looking at it.
1) Defending is special, and doesn't need the enhancement bonuses to remain to still apply. However others, like flaming, etc. do and fade away.
2) A sword has to have an enhancement bonus to get a special ability, not to keep it. So all special abilities still apply.
3) You just can't. The description is slightly in error, and you have to keep the +1 at least.
Who said I had to transfer the magical bonus?
As far as defending is concerned, the adamantite enhancement is just as good as the magical ones. Why can't I transfer the +2 from the adamantite, and just have a +1 or +2 magical weapon? Can't see any thing in the books to say you can't. For those who need some realism to see it, think of adamantite as just having an inner, different type of magic than normal magic that gives it its special hardness and enhancement, that can be transfered all the same.
If I transfer the bonus from a magic weapon, do I still get the +1 to attack for it being masterwork?
If you believe my argument above, the answer is yes. I had never thought about it before, but looking at it I agree, you still get the bonus.