Magic Weapon

[AsheItachi]

Does casting this on an already magic weapon say
Short sword +1

Stack making it a
Short sword +2

Till the end of the spell?

[Flickerdart]

No. The bonus granted by the spell and the bonus inherent to the weapon are both enhancement bonuses, and do not stack.

[Killer Angel]

Of course, a greater bonus will overcome the lesser.
So, if you cast a Greater Magic Weapon for a +2 bonus, your short sword +1, will become a +2 for the spell's duration...