This sounds like the "compatability files" problem again.
1) Find the Savegame folder for your mod. Use Windows Explorer or File Explorer to do it. The Savegame folder is in Paradox Interactive:\ Darkest Hour:\ [YOUR MOD HERE, such was Darkest Hour Full or World In Flames]:\ scenarios:\save games. This folder should be full of saved games, but the NOT one you are looking for.
2) Look for a tab or button marked "Compatability Files". Click on it.
3) The other files should disappear, and the files you are looking for should appear. If not, you are in the wrong place or have a different problem.
4) Copy the files you are looking for, but do not paste them anywhere.
5) Close the Window Explorer or File Explorer you are using and open another one.
6) Repeat step 1 but NOT step 2.
7) Paste the files you copied in with all the other saved games.
8) When you run Darkest Hour now, your saved games should appear.
I am sorry this is long and difficult, but I wanted to break it down into simple steps.
I do not know why this problem happens or what can be done to avoid it.
Good luck!