As you all I suffer from this problem also. Tired of loosing SMS, I have copied the SMS to the PC using PC Suite, then deleted them all from the phone and then put them back to the phone.
I realised two things: on PC Suite the messages had the correct destination / sender; after deleting all on the device, one SMS was seen on the Nokia Suite as being still on the phone but could not be seen from the phone...
Looks like the storage of the SMS is OK but the client mess up reading them...
Anyway, now all the SMS are OK in the phone, even the old ones, until the next time the Messages Client of the N9 becomes lost again...