I have found that after receiving an update, if you have any new problems, they are often fixed by pulling the AC plug for 20 seconds (when you are not recording and when there is no recording scheduled for the next 5 minutes or so).
It is doing this with Lost for me thus far. I recorded the two hour premier last week.
On Saturday, the first part of the premier was shown with all the comments and stuff ... my timer wanted to record that one.
And the lest night, they showed the second part of the premier with all the comments and stuff ... my timer wanted to record that one too ...
We wound up having the EHD being not recognized any more, plus we lost our "custom guide" channel lists & timers.
We've re-done the timers & custom channel lists but still have the "old" EHD which is going to wind up (hopefully) getting a recovery job on, one way or another.
I whined about it here: backing-up-usb-drive
'cuz that was the most appropriate related thread I could find after a 30 minute search.