This study examines the rhetorical structure and thematic progression patterns (TPP) in the Introduction and Discussion sections of Iranian dentistry research articles (RAs), exploring alterations after copyediting. Using a focused corpus of 20 RAs and their pre-edited drafts, suitable for in-depth rhetorical analysis, we investigated macro-structures via Swales’ (2004) and Hopkins and Dudley-Evans' (1988) model and micro-structures via Daneš's (1974) TPPs. The results showed that Introductions were generally well organized, with nearly all articles establishing research topic and the vast majority stating a specific contribution. In contrast, Discussions frequently failed to realize the expected interpretive and evaluative rhetorical functions, especially those related to accounting for the results, exemplification and situating the findings within wider disciplinary knowledge. While copyediting had limited influence on rhetorical coherence or thematic continuity of the Discussions, it markedly improved thematic continuity of Introductions in over half the cases by mending the disrupted TPPs.  The results have direct implications for English for academic purposes (EAP) teaching and editorial practices, highlighting the need to move beyond formal adherence to prescriptive Move models, towards prioritizing the development of evaluative competence and rhetorical judgment in non-native English-speaking (NNES) authors.