Swap the box. I know you've invested time building your library, but it's either tolerate the dropouts on approximately 3% of your recordings or replace the box. It don't cost nothing.
I read on avsforum the Cisco 9865HDC was recalled for issues with drive firmware and DVR heads. That was a few years ago and I'm sure Cox successfully recalled all boxes and Cisco successfully repaired all boxes. However, when boxes are on the bench for repairs, mistakes can happen. That's a small percentage but a percentage nonetheless.
Even new boxes from the factory have a small percentage. I got a new box once but its HDMI port was dead. How's that happen? It happened.