What has most likely happened is that the Heater-a/c unit needs to be recalibrated and here are the steps to do so.
With the engine running and fully warmed up, A/C has to be turned off for at least 5 minutes [don't turn it on at all] and transmission in Park do the following
1. Set the temp control all the way to cold
2. Set the mode selector to Vent so air blows out of the dash panel outlets.
3. Hold down the rear washer button and the rear wiper buttons simultaineously for about 5 seconds until most all of the heater and ac panel lights blink and then release both buttons
6. At this point the system should go into a self calibration test which can take up to 60 seconds. While it is calibrating various control panel switch lights will blink as it goes through it's tests.
7. When the system is done calibrating then just the rear wiper light should be flashing and you can exit the test by turning off the vehicle. Wait about 10 seconds and restart the engine and it should be fine. If both the rear wiper and intermittent light are both still flashing after the calibration then there is most likely a problem with the system that will need more diagnosing. I see this fairly often with battery replacements so I think you'll be ok. It sometimes takes a couple of tries to calibrate so don't give up if it doesn't work the first time. Good luck, hope this helps!
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