I have managed one improvement. iTunes has stopped deleting the apps that aren't synced.

I don't know whether it was something I've done or whether it was a change in iTunes 9.1 that I installed today.

That change does at least make it just a minor inconvenience again, as I can now let it sync the rest of my data without it deleting my apps. Let's hope it stays that way...

I'd obviously still love to solve the underlying problem. Does anyone know if there is any extra logging I can turn on ? (not that there'd probably be any settings I could change if I located the problem)