I think you're going to have to bite the bullet and restore the links manually.
I worked in a marketing dept a few years back that did the same thing in their illustrator files, so when I'd go in to work on older files, it'd give me the same "would you like the search for this file?" flak you're getting (happens a lot in quark, too, but that's because quark sucks in general). I remember not finding any other way to do it.
So yeah, it's a shitty proposition, but that all I got.
"...And my quarter is ruined. My business lost about 200K in revenue.
On a positive note, I did save some money on car insurance by staying with GEICO..."
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