The Tomas paper seems to conclude that there is no difference between ME/CFS patients and healthy controls when it comes to mitochondrial complexes. So Tomas et al conclude the mitochondrial dysfunction must be upstream of the mitochondrial respiratory chain:
Indeed they do contradict each other. This study addresses all of this, including (2) papers by Tomas. Remember, this study was done on EBV infected cells. They mention that they "resolved these inconsistencies by revisiting the issue of mitochondrial function and capacity in immortalized lymphocytes (lymphoblastoid cell lines or lymphoblasts)."