Better late than never
I've found the bug and solved the problem.
The solution is: DELETE UserPath.ini
I don't know why that file was added (it wasn't in earlier games) but it spoils the party.
When it's removed - Modpath.ini starts to work correctly.
Modpath.ini was used in earlier games and it worked.
So it is simple: write mod name in Modpath.ini (here: Ngc), save it and game will be storing all save, log and scripts files in game folder xxxx\Wars of Napoleon\NGC\
Tested with other Ageod titles (Cw2, TYW).
Meteoryt-like user. Strikes and disappears.