I suspect you'll have to edit the file path inside the atmosphere file like this:
$Sky::sunFlareTopTexture base/lighting/corona2.png
$Sky::sunFlareBottomTexture base/lighting/corona2.png
to
$Sky::sunFlareTopTexture add-ons/youraddon/yourcustomflare1.png
$Sky::sunFlareBottomTexture add-ons/youraddon/yourcustomflare2.png