I am not sure about the SRX CLI, but I assume the commands will clear all IKE SAs.
From the SSG side, you can clear the SA as well as the session:
get sa | i <<IP of the SRX>>
In the output that gets printed, you will see an ID fiedl - the first one from left. Clear it with the command ==>
clear sa 0x<ID you see>
To clear the session, you can find the session id by: get session src-ip <SSG> dst-ip <SRX> or the reverse. Then clear it with the command: clear session id <ID you see>
If this still doesn't help, I'd recommend opening a case with JTAC.