HI Bojalu

So sorry I haven't seen your message until now.
Sounds like a pretty unpleasant situation

Can I recommend that you do any future work on these outdoors, for starters.
If you have access to a vacuum cleaner (preferably with a HEPA filter but not essential), put it on the absolute lowest suction possible. If you can find a set of mini attachments for your cleaner, even better. Otherwise, get the softest end to your hose (there's usually one with a little brush on it) and get an old stocking/pantyhose and cover the end of the hose with it. Hold in place with an elastic band. On VERY low suction, wearing rubber or vinyl or latex gloves, long sleeves and a mask, and standing upwind of your documents, start cleaning them by loosening the dust with a brush in one hand, and sucking the dust up with the vacuum held in the other hand. If the stocking covering clogs up too much, you could try without it but make sure the documents (or loose bits thereof) are not likely to get sucked up into it.
Once the dust is gone, open out the documents and leave them outdoors on a nice sunny day (not blazing hot), to air. This will get rid of mould spores and start getting rid of the smell, too.
You could try putting the documents in a sealed container (such as a plastic tub) with an open box of bicarb soda in it (not in contact with the documents). I've had some success reducing smells in documents using this method.
Good luck!