Vegepygmy said:
Actually, this question arises even before the GMW spell is cast.
Indeed. And I'd say yes - the masterwork enhancement bonus can still apply

(This was less debatable in 3E, where the +1 granted by the masterwork quality was not an enhancement bonus, and therefore could not be interpreted to be affected by the transfer. But in 3.5, I'd still argue that the 'some or all' clause provides for transferring the magical bonus while leaving the masterwork bonus in place.)
Of course, there's one other Defending question we haven't revisited in this thread.
If you transfer all of the weapon's enhancement bonus away, it is temporarily not 'a weapon with at least a +1 enhancement bonus', and so it is no longer eligible to possess the Defending special ability.
This would mean that transferring
all of the enhancement bonus would result in the weapon temporarily becoming a non-Defending weapon, which would result in the enhancement bonus returning, which would result in it becoming once again a Defending weapon... but since it's no longer 'the start of the round', you can't reallocate it.
To actually gain an AC benefit, you would of necessity leave at least one 'plus' untransferred, so the masterwork issue would never actually arise.
-Hyp.