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first, you'll want to try changing the channels on the controller. To do this, hold the up and down arrow on the controller for 5 seconds. You'll see the display show you the number channel you're currently on. At this point, use a screwdriver to open up the jbox. You should leave it connected to the Aqualink RS power center. Once you have it open, flip the switch entitled "LEARN" to the ON position, then press the reset button. You should see some blinking inside the jbox. Change the channel on the controller using the up and down arrows. Any channel will do. Once this is done, you'll see the light inside the jbox turn solid. Turn "LEARN" to the off position, and hit the reset button inside the jbox. This will reset the connection.
If this does not work for you, turn the power off completely to your power center at the breakers. Open your power center and flip down the front board. On the back of this board you'll have a 9v or CR2032 battery. Replace this with a new battery. Make sure that when you pull the existing battery out, you allow a minimum of 30 seconds to pass before putting a new battery inside. Close the power center and turn power back on.
If the issue persists, you may have a failed front board, the RS485 connection can be bad on either end, the wires can be bad, etc. Typically, changing the channel and/or replacing the battery will resolve the issue. Good luck!