First: Skin manager can detect Forgotten Battles, Pacific Fighters and 1946 as seperate installation. all at one time at the same computer.
Now, it can only detect one installation of 1946. You cannot fake it by making it believe that the other BBB 1946 is Forgotten Battles. That will give issues.
Now it detects the path of the 1946 version as it is officially installed throough the installation program. Not the copies you made.
You can select another installation manually. To do this go to the Tools menu and then Configuration. On the last page of this window select the path of the installation you like for "1946 path".
Making this path empty again should make Skinmanager read the path from the official IL-2: 1946 installation information again.
Your skins might be lost in a directory you used for the initial installation?
Automatic skin installation only works if the skinner suppotrs it. That would be my packages and some very old packages made by CanonUK and Hammerd. Unfortunately little skinners make effort to use the tool and make their fans happy
I hope this answer solves your issues.