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I have a houserule that every magical weapon, shield or armor has some kind of "focus" (a gem, a bone, a holy symbol) in which the actual magic resides.
Those can be separated from the weapon and attached to another one in a process that takes one hour per +1 enchantment, costs 100 gp per +1 and needs a spellcraft-check with a DC of 15+ enchantment bonus.
Every item can have only one focus attached and must be masterwork.
Foci can be merged in a process that takes 1 hour for every +1 of the end product, has a spellcraft DC of 15+1 per enchantment of the end product and needs magical materials worth the difference between the combined worth of the original foci and the end product.
While combining or transfering foci, the crafter can decide to keep the original magical effect or turn it into a flat enhancement of appropriate strengt (so a +1 flaming focus could be made a +2 focus). None of these rules can be used to exceed the usual limitations on item enchantment.
If the spellcraft check fails by 5 or more, the foci are imbalanced by the process and are inert for 24 hours.
This solves the problem of believability, lets the players keep their "ancient familiy heirloom sword TM" and even gives them the option of switching a focus between weapons if they have a lot of time to prepare for a fight and know about a certain DR or somwthing but also carries the risk that they botch the roll and are completely bereft of their magical weapon for a day.
Also it adds cool details to the weapons, because every Focus is unique and you might end up with a fighter in shiny armor who has a focus made from a human fingerbone attached to his weapon, because he took it from a goblin chieftain.