Okay, I've tested on 1.06.1 (from !MainLog.txt: 10:11:14 (Reporting) Game Engine version: CW2 1.06.1 (August 17th, 2016)), and I ran 5 turns. Not one missing regiment (32 are missing) has be replaced.
If anybody wishes to try this out themselves, here are the files you need to install the scenario: https://www.dropbox.com/s/c581gfae8zzcof2/ReplacementsTest2.7z?dl=0
Installing the scenario is completely safe and will affect nothing else in the game other than being able to play the scenario.
Copy the following files into their locations:
'CitiesReplacementsTest2.inc' --> '..\CW2\Includes'
'LocalStrings_CW2_ReplacementsTest2.csv' --> '..\CW2\Settings'
'ReplacementsTest2.scn' --> '..\CW2\Scripts'
'ReplacementsTest2.sct' --> '..\CW2\Events'
'Script.ini' does not need to be installed, and is included in case anybody wishes to mod the original setup. Understanding modding setups is a prerequisite.