We have a +1 short sword that has 15 hitpoints. It has taken 10 damage. How much should it cost to repair that damage?
A damaged yet not destroyed magic item can be repaired for free with the spell mending or the spells make whole et al., yet the caster's level must at least meet the magic item's caster level. Further, a creature employing a scavenger's stone can effect repairs to objects at will, restoring 1d6 hp to an object per full-round action the stone's rubbed against it. However, the stone's 2,000 gp price is fairly substantial for its effect, even though the stone seems to care neither if an object's mundane or magic nor, in the latter case, about the object's caster level.
A creature that possesses the appropriate item creation feat (like this one or this one, for example) can make like new a destroyed magic item that the creature could also create—the prices in time and gp are half the original item's creation costs—, but a creature that possesses an item creation feat doesn't seem to be able to repair hp damage that's been dealt to an appropriate magic item. (This reader suspects this oversight is due to dented and dinged magic items usually functioning as well as undamaged magic item, so there's often little need to repair them until they're actually destroyed, but this player totally understand your paranoia!)
Expanding the mandate of item creation feats to include repairing damaged-yet-not-destroyed magic items seems like an extremely reasonable house rule, though, but—to be clear—it's one this GM has never needed to implement. That said, were a player to ask if his PC's item creation feat could be used to repair a damaged but not destroyed appropriate magic item, I'd consider a house rule that determined the price to fix each hp of damage dealt to a magic item as the price to repair that magic item fully divided by the number of hp the magic item possesses and every fraction of 1,000 gp taking the craftsman 1 day. For example, a +1 shortsword normally has a cost to create of 1,155 gp therefore to repair it fully would have a price of 577 gp 5 sp and that means each of its 15 hp can be repaired by paying 38 gp 5 sp (or 38 gp if the GM considers this a fraction and rounds down), and the weapon could be repaired from 1 hp back to its full 15 hp in but 1 day.
Nonetheless, this still may be too expensive. In the abstract universe Pathfinder creates, repairing a magic item while it's not destroyed should probably have a price that's significantly lower than the price of returning it from its destroyed state to its functional state. (By way of analogy, in much the same way that a cure light wounds spell can be used to keep a creature functional, but a raise dead spell is needed to bring a creature back from the dead!) In that regard, it's perfectly reasonable to reduce that computed price-to-repair-per-hp by 3/4 or 1/2 or even lower.
Magic Items must be repaired magically. There is no caveat for non-destroyed, but it would be a fair ruling for a GM to "pro-rate" the damage. However, without a homerule, you must simply pay half the crafting cost (or learn/buy casting(s)) of Mending or Make Whole:
Repairing a magic item requires material components equal to half the cost to create the item, and requires half the time. The make whole spell can also repair a damaged (or even a destroyed) magic items—if the caster is high enough level.
Your example, a +1 short sword has a total cost of 2,310g, crafted cost of 1,155g so it would cost 577g 5s to repair.
One or more Mending and/or Make Whole spells can accomplish this at no cost, at at least CL 3. If the sword were destroyed (0 hp), you would need to be CL 6 or greater to restore its magical properties with Make Whole.