If the SunSaver Duo LED is flashing Red and has stopped charging, it may be due to an RTS (Remote Temperature Sensor) fault. The RTS terminals on the upper left front of the controller can be susceptible to accumulating dust/moisture/debris. If these terminals gather enough dust/moisture a resistive connection across the terminals can form. To the controller, this resistive connection may seem as though a damaged RTS is connected. If there is no RTS present, the issue can be fixed by:  – removing battery power from the controller  – using a small piece of wire to connect the two RTS terminals together – reapplying battery power with the small wire connected (keep the wire installed until if/when you decide to install an RTS probe into the system).
Newer SunSaver Duo controllers come with a metal jumper pre-installed to help prevent this issue.