I didn't count Hill or McLaws in the wake of the Seven Days.
Holmes was returned to district command in North Carolina after the Seven Days (particularly a bad performance at Glendale) and then picked by Davis to replace Hindman in the Trans-Mississippi. Magruder was initially slotted to take command of the Trans-Mississippi before the Seven Days but had delayed his transfer until the battles were fought. Then, amid allegations of misconduct afterward, he delayed again to try to get a court martial. This cost him both the departmental appointment and a spot in Lee's army and in the end he was shuffled to the District of Texas. Huger, unfairly blamed for the draw at Seven Pines, actually performed very poorly at Glendale and was reassigned, with R.H. Anderson taking his place. He was the one officer who removed from a division in Lee's army who had not been assigned to another department originally. He assumed duty as an ordinance inspector in the District of Arkansas and then the Trans-Mississippi as a whole. Whiting became ill during before the Second Manassas Campaign, with Hood taking his division. Whiting had antagonized President Davis and Hood performed so well that Whiting was not returned to the post, and was instead assigned to Fort Fisher and the defenses of Wilmington.
Wilcox was still in the Army of Northern Virginia but had lost command of his division after an illness and a poor showing at Second Manassas (it was folded into Anderson's). He was unhappy when Pickett was selected to take D.R. Jones's old division and was promoted over him and sought re-assignment in the West. Lee convinced him to remain, but he still commanded a brigade in Anderson's division until Gettysburg. After this, he was promoted to take the Light Division after Pender's death.
Other officers who were reassigned out of the army include Thomas Drayton, an incompetent brigade commander who was sent to the District of Arkansas.