Using NormalizeExp in Two Heroes causes problems in the Pokemon table index where two Pokemon get merged into the same index slot. This often causes Shigezane's Pokemon to be replaced with some other Pokemon in the player's army.

As for the reason this affects Two Heroes and not other vanilla episodes, there are two possibilities that immediately came to mind. Two Heroes is special in that
-it has the fewest unassigned warriors of any episode. However, removing warriors did not solve the issue
-it is the only episode with multiple recruitable rank 2 warlords. This seems most likely to be the cause

I played the episode so many times before I realized that the issue did not occur unless I used the lua script

Baconfry:

For testing purposes is it possible to create a lua script that erases all of the selected warrior's pokemon except the one they're currently using? (Unless IsLegendary = true)?