We just had this issue on a AC16 project. No problem on Friday, but came in Monday morning to find the (OS X) server itself in a very poor state. Very low responsiveness, and the share points were incomplete and had to be reshared. BIM Server started normally once the server was sorted out.
But upon trying to Open the already joined project from Friday, we got "Project has not been shared yet". Well, it is shared, and not only that we can see ourselves as Joined in the Project Settings in Server Manager. At this point it is clear we need to bail out and reshare the project from a backup PLN.
Except the backup list is distressingly empty. No manual or automatic, no PLN or BIMProject. In the Backup Schedule the PLN checkbox has unchecked itself (we would never uncheck it). The BIMProject box is checked, but still, nothing in the list.
Thankfully the backups were there (both kinds), in the expected folder of the project path, and we able to recover the work. Since yesterday the backups have been taking place.
So all is well in the end, but this issue is still alive in 16 at least.