My S&R timers disappeared with the S209 update also. I tried to reload them from the remote. The restore reported success but the S&R timers did not restore.209 on both Hoppers as of yesterday AM. I had 3 Seek timers which were victims of the update, all normal DVR timers survived.
I tried re-entering the 3 Seek timers but I'm not convinced they're working yet (one of them definitely had matches before the upgrade but didn't after I re-entered it).
S209 has a new bug when creating a new S&R timer: A conflict resolution screen appears but lists no conflicts. You must press Save (red button). Then you are taken to the Viewing Status screen. When you return to the Timers screen, the newly created timer does not appear. You need to exit then go back in.