The mission files are really just text files. You can copy, remove, scramble them all around. What matters is that the mission files are located in the correct folders. So for example IL-2 1946/Missions/Single/DE/Bf109/ should contain a single mission for the Bf109 flying for Germany. Actually the last part doesn't matter at all... anything could be there so long as it's a mission file.
It doesn't matter if the mission file was made with IL-2 1.0 or IL-2 1946 4.11. Mission file format hasn't changed in any significant way and I've tested many missions that were done on older versions with absolutely no problems in terms of the mission loading and running.
AI and flight model changes sometimes affect the mission design... but as far as the mission loading and working there are no problems.
What is the error or problem that you are having? I'm having difficulty figuring it out.
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