Well I am dead confused about this one. One minute everything is working a treat, the next... my custom themes and modules have disappeared! Apart from FeauturedItemSlider all my other installed modules are gone and the theme has defaulted to SafeMode.
The site is running Orchard 1.4.1 on azure with multi-tenancy. The default site and the tenant are both still there. Connectivity to the storage account and the db are still ok too.
Apart from having been hacked (how fast will I get cracking on getting SSL on the sign-on page now!) or little green men from outer space I am not sure what to think.
I am about to upload the missing modules and themes again because there is literally not a trace of them on the server.