Green phlegm usually, although not always, indicates infection. This phlegm could be coming from your sinuses and/or your lungs. It would be unrelated to your lupus. It may be a sign of a non-infectious, hypersensitivity or allergic problem such as allergic bronchopulmonary aspergillosis (ABPA).
To find out what could be wrong your phlegm needs to be carefully examined, both under a microscope and by culture. It should be cultured for bacteria, fungi and mycobacteria. A CT scan of your chest may show if there is another problem effecting your lungs.