Still no idea what caused it, but we resorted to typing all the contacts back in
To try and avoid future occurences, we've both installed an app called 'My Contacts Backup' which will capture all your contacts off the phone and embed them into an e-mail (which you send to yourself) as a .vcf file. Obviously you need to do this on a regular basis if you add contacts frequently
NB - if your computer is not a Mac, the e-mail will arrive with an attachment which when opened appears to only hold one record
If you're on a Mac, apparently the file does indeed hold multiple contacts
Our solution - send it to yourself to a mail address that you have set up on your iPhone and then basically keep the e-mail stored in the inbox on the phone
Should the situation occur again, just open the attachment and the saved contacts will be immediately uploaded back to the phone
We don't sync contacts on iTunes (which would obviously be another option) as we both use the one PC but have different contacts (including my business contacts which are synced by a Microsoft Exchange server as well over the air)
Not a solution as such to the problem, but at least we now have our contacts saved outside of the contacts section of the phone
Also updated my wife's phone to iOS6 and haven't had any problems since, but I'm not sure that's the issue really