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From your description I am pretty certain that you are not extracting the IGC into your main EU folder, allowing it to overwrite any files it wants to.

From my experiments it only uses the first one and the igcconfig file doesn't work until I manually move the files from the IGC scenario folder to the original Scenarios folder).

If you correctly extract the IGC zip into your main EU folder there will not be two scenario folders. Just the one.
 
Oh, and the .kri file is not used by the game, but it will show ID conflicts, just as the .pru and .bra files will if you turn on the "Unified Prussia" option and run EuCheck.

You might as well delete the .kri file.