How can the Hadith which mentions that some of the good deeds of the Prophet's ﷺ Ummah will be like scattered dust if they violate Allah's prohibitions in solitude, be reconciled with the Quranic verses and Hadiths that affirm that whoever does an atom's weight of good will see it, and that good deeds efface evil deeds? And do sins committed in secret completely nullify good deeds done in secret?

The nullification of good deeds by bad deeds is a balancing nullification. Just as good deeds remove bad deeds, so too can bad deeds remove good deeds. Thus, for those people whose sins in secret were many, and who outwardly showed their disregard for God's awareness of them, their bad deeds nullified their good deeds. There is no contradiction between this and the Almighty's saying: "So whoever does an atom's weight of good will see it"; because he will see it, but he will see it nullified by bad deeds. Polytheism is what nullifies all deeds, whereas sins nullify only the good deeds they correspond to and do not nullify the entire deed.