Welcome to the forum, Andy.
This is a common problem. Just because a model is built a certain way, there is no assurance that the drawing was structured the same.
Not knowing what you are using makes this a best guess, but in general, a STEP export format will preserve the product structure the best. Other formats will also try to preserve the structures. You client just has to give you the model file at the top level and it should be properly structured with subassemblies and components below that. However, be aware that the same item may be exported as unique instances. Meaning you will have some work to do for rebuilding things to reuse common parts.
What can I say, you have to evaluate what data you have available. There is also significant effort going on at PTC to make Creo 3 more compatible with other systems, including 2 way communication. If this task is big enough or complex enough where preserving associativity is a huge advantage, you might catch up with what's going on in development and PTC schedules. A value added reseller might just get you and your client up and moving in short order depending on where the development team is at the moment. This could be a a win-win (&win) if your client's representative has some clout with PTC.