If I only had a memory...
I know I've read something, somewhere, about 'repairing' magical items. If I'm not totaly off it costs 1/2 the 'new' cost of said item. I think the rational behind this rule was based on recycling/reusing the materials/magic in the item you have, thus halving the costs involved in the items (re)creation. I believe that, in that same rules 'area', it was mentioned that (as a house/optional rule) that you could use the same rule to essentially 'recharge' a limited-use item.
This is pretty-much how I'd handle this question, if my group were still playing that is. It doesn't seem too terribly unbalancing either, and makes some sense in that you've already done the truely 'hard' part of making a mundane item magical, ie: you're enhancing what's already there and not starting from scratch.
Another thing to keep in mind is this: How many players would prefer the recharging of their Wand of Magic Missles (5th) (when they got the Feat) over 'upgrading' it to a higher caster level when the original ran out of charges? I know my character would prefer the higher powered versions, anything else would be sacrificing too much in way of firepower.
Hatchling Dragon