Actually, that's the sort of thing you should be talking about before taking on a project. If your rig can't handle the sample rate they want you to work at, then you shouldn't be doing the job. They're not going to want to convert to 48k if they're working in 96k just for your benefit, they're going to hire somebody that can do what they want.
Not to mention, going from 48k BACK to 96k is pointless. You've already lost whatever info was there by halving the sample rate, you don't gain any quality back by up-converting again, you should just leave it in 48k. In my experience, 44.1/48k are still the default sample rates for anything "pro" (TV, Film and Albums), 88.2 and 96k (and up) are mostly marking hype, and for the most part just lead to problems with having to do a bunch of file conversions, similar to what you've discovered.
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