From: Combat Information Center
I just tested this...Set up a Battle between Germany (Player 1) and Soviet Union (Player 2) in June 1944. The Germans set up on the left, the Soviets on the right. The German retreat and reinforcement flags were on the left side, in the middle of the map. The Soviets' flags were directly opposite, on the right side.
Set up another Battle between Germany (Player 1) and US Army (Player 2) in June 1944. The Germans set up on the right, the US on the left. The German flags were on the right side in the middle of the map, the US's were directly across on the left side.
Using the editor, I took a custom map and placed the German retreat flag near the top of the left side of the map, and the US retreat flag near the bottom of the right side. Saved the map in a new slot, then set up the same Battle as above. When deploying, the Germans set up on the right side, and their retreat flag was in the middle of the right map edge. The US set up on the left, and their retreat flag was in the middle of the left map edge.
I can only draw one conclusion: the retreat and reinforcement flags are solely dependent on the nations and date chosen, and are set when the player enters the Deployment phase. The flag position information is not saved as part of the map, unless it is inside a scenario fileset.
This being the case, I don't see how you could alter the map DURING the PBEM Battle setup; only if you can change the email files to scenario files, make changes, and then back again might it be possible.