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If you try to override that, you run the risk of creating an infinite loop. At the very least, you would be denying your users access to the frame-busting page.
I think you need to locate the source of this behavior rather than try to override it.
I know he said he doesn't have any framebuster scripts (that's probably a good bet -he would know), so he should be willing to do a search for the "target=" attribute and find any potential problem pages. If that doesn't uncover the problem, you might talk to some of your more savvy users and ask them to notice when the navigation frame vanishes.
However, if I misunderstood and your users have a wider range than just one site, then option two is about all I can offer you. If your users really miss the navigation frame and you can't find the source of the problem, you might give them a bookmark to return to the framed set-up.
And you might also just poke around, navigating for yourself. If this happens frequently, then you may just stumble over it.