Sorry i cant help with the exact problem so this is more of a question rather than a solution...
You/your client does have a backup of their site. yes???
There are lots of businesses and web site owners now-days who actually have a fully functioning copy of the site at another url location. That way one can simply change the dns records and voila...shes all good again. Then one may stuff around with updates/upgrades till the cows come home without worrying about taking the site down if there's a "cock-up"
Anyway, not a solution but food for thought