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I thought this would be a very easy mod. I simply wanted to edit the initial unit disposition file to make Lee the commander of the ANV instead of Johnston.

However, when I changed Johnston's name to Lee's (following the naming convention), all that did was eliminate every pre-assignment in the scenario (for example, all generals were unassigned to divisions, including McClellan, Halleck, Grant, etc.).

I am almost certain that if Lee started as commander of the Confederate forces in northern VA, he would stay commander of them because there is a small chance of the AI using him on its own (usually its Jackson or Stuart though, with Longstreet seeming to be the third most popular choice).

I can't tell you how much more immersive the game is with Lee commanding in Virginia than Major General JEB Stuart, who wasn't even a significant commander until the Peninsular Campaign.

It sounds like you did something that affected the file overall. Which file(s) did you change, and what exactly did you do?

The ACWCommanderAssignments File reads:
 
// Union 
// Army_Potomac_Left 
Banks,_N.P. Banks'_Division
McDowell,_I. McDowell's_Division
Heintzelman,_S.P. Heintzelman's_Division
Porter,_F.J. Porter's_Division
McClellan,_G.B. Army_Potomac_Center
Franklin,_W.B. Franklin's_Division
Hooker,_J. Hooker's_Division
// Army_Potomac_Right 
Smith,_W.F. Smith's_Division
// Forces not in Potomac River 
Buell,_D.C. Dept._of_the_Ohio
Hunter,_D. Dept._of_Kansas
Halleck,_H.W. Dept._of_Missouri
Grant,_U.S. Dist._of_SE_Missouri
Rosecrans,_W.S. Dept._W_Virginia
Wool,_J.E. Dept._of_Virginia
// CSA 
Johnston,_J.E. Dept._N._Virginia
Beauregard,_P.G.T. Dist._of_the_Potomac
Holmes,_T.H. Aquia_District
Jackson,_T.J. Valley_District
Magruder,_J.B. Army_of_Peninsula
Johnston,_A.S. Army_Central_Kentucky
Buckner,_S.B. Army_Central_Kentucky
Polk,_L. Dept._No._2
Bragg,_B. Army_of_Pensacola
Floyd,_J.B. Army_of_Kanawha
Loring,_W.W. Army_of_Northwest
Price,_S. Missouri_State_Guard
McCulloch,_B. Army_of_the_West
Zollicoffer,_F.K. Army_Eastern_Tenn.
Marshall,_H. Army_SW_Virginia
Lovell,_M. Dept._No._1
 
I changed it to:
 
// Union 
// Army_Potomac_Left 
Banks,_N.P. Banks'_Division
McDowell,_I. McDowell's_Division
Heintzelman,_S.P. Heintzelman's_Division
Porter,_F.J. Porter's_Division
McClellan,_G.B. Army_Potomac_Center
Franklin,_W.B. Franklin's_Division
Hooker,_J. Hooker's_Division
// Army_Potomac_Right 
Smith,_W.F. Smith's_Division
// Forces not in Potomac River 
Buell,_D.C. Dept._of_the_Ohio
Hunter,_D. Dept._of_Kansas
Halleck,_H.W. Dept._of_Missouri
Grant,_U.S. Dist._of_SE_Missouri
Rosecrans,_W.S. Dept._W_Virginia
Wool,_J.E. Dept._of_Virginia
// CSA 
Lee,_R.E. Dept._N._Virginia
Beauregard,_P.G.T. Dist._of_the_Potomac
Holmes,_T.H. Aquia_District
Jackson,_T.J. Valley_District
Magruder,_J.B. Army_of_Peninsula
Johnston,_A.S. Army_Central_Kentucky
Buckner,_S.B. Army_Central_Kentucky
Polk,_L. Dept._No._2
Bragg,_B. Army_of_Pensacola
Floyd,_J.B. Army_of_Kanawha
Loring,_W.W. Army_of_Northwest
Price,_S. Missouri_State_Guard
McCulloch,_B. Army_of_the_West
Zollicoffer,_F.K. Army_Eastern_Tenn.
Marshall,_H. Army_SW_Virginia
Lovell,_M. Dept._No._1
 

I must have made a typo originally.
 
I tried again and it worked as written above.

Oh, great. I was thinking that maybe you hadn't used Excel (or similar program) properly. If you save the wrong way that would probably mess things up.

Let us know whether your experiment works. I expect it will, but am unfamiliar with the code.

I restarted four times and Lee remained ANV commander each time after the first turn.
 
I kept playing one of the restarts into 1862 and he's the commander.  So that's the way to do it.