now I have deactivated the automatic annual renewal and now I no longer have access to the content.

They cancelled their subscription then. If they did that from within his PayPal account then PayPal will send a cancellation IPN and we'll cancel their subscription as a result of that. There's a button within CBSubs for them to cancel just auto recurring payments. They have to use that button to only cancel recurring payments.

I checked and his payment was showing in the CB logs, but his paid membership status was GONE. I had to reset him as a paid member. It's fine now...

You should still see their subscription within CBSubs > Subscriptions, but it should be in a cancelled status. The only other thing I can think of is they cancelled it at PayPal before PayPal notified CBSubs that a payment was complete, which would probably cause some goofy issues we can't really account for. I suggest maybe offering user choice on auto recurring so they don't attempt to cancel right after subscribing.