Thought I'd better update this in case this does happen to someone else.
I have now received all my documents back. Apparently it is relatively common for them to send the passport of the applicant back separately to some of the supporting documents (though I still don't understand why, as they have to pay two lots of courier fees).
If you do have problems with this, don't waste your time calling the TLS number as it appears to be staffed by a single person who is utterly powerless to help (and is not even based in the same city as the rest of TLS). What you need to do is email the consulate directly:
visas.londres-fslt@diplomatie.gouv.fr
When I did this I had a telephone call back within 3 hours and the lady was very helpful, tracking down my passport and calling me back with a tracking number once it had been despatched.
So for me, it has all ended well. We have all our documents and my wife has a multiple entry Schengen visa. Thanks for the good wishes on here, hope things work out for you too.