Lime configures settings in “C:\Users<your user name>.lime\config.xml”, but it’s possible that HXCPP has a setting that is overriding your choice in Android NDK.
Check “C:\Users<your user name.hxcpp-config.xml” as well. You may be able to delete or update the Android NDK path set there
That might be enough, but if it is not, you will need to either update, or clone Lime from the source (at your same version) and rebuild it yourself.