Gen. Manigault's figures for one brigade (his own) may be instructive here. At the beginning of the campaign, roughly 1,900 officers and men were present for duty. During the course of the campaign about 200 members either joined or returned for a total of 2,100. At the end of the campaign the brigade counted only 600 present.
Let's look at O.R. ser. I, vol. XXXVIII/3, p. 677. Tell me if I'm reading this page incorrectly, but it looks as if aggregrate present for the Army of Tennessee and Army of Mississippi for June 10, 1864, totals 106,876 for infantry, artillery and cavalry.
Aggregate present includes those actually present for duty, plus those on extra duty, sick and in arrest. In other words, all those in camp with the army. It doesn't include prisoners of war, those absent on detail, absent sick or anyone else absent, with or without leave.