My understanding is that he was legally forced to hand over the encryption key and all the data. The FBI, then, could have read all messages that were available on the server.
He shut down so that no additional mail could be sent and read.
It's unclear to me how much mail was kept on the server. Only unread mail? Anything in your inbox? Everything?
My understanding is that the key he was forced to hand over was the TLS key that protected communications between clients and his server, and the stored emails were encrypted with a key derived from the user's password.
So whether or not the FBI could read a particular stored message or not would depend on whether they'd been able to obtain that user's password: they could if the user had logged in after the FBI had the certificate, or if they'd logged in using a non-PFS cipher suite at any time, or if their password was vulnerable to cracking or determinable by the FBI in some other way.
He shut down so that no additional mail could be sent and read.
It's unclear to me how much mail was kept on the server. Only unread mail? Anything in your inbox? Everything?