The problem I was experiencing wasn't caused by your mod. I was using nicefill mod as well, since I don't like the look of the landfilled tiles. That mod causes that every time I place landfill, it replaces deep water tiles in its surrounding with shallow water tiles.
I actually wasn't expecting that small mod to cause me that issues. I was rather expecting large overhaul would cause this.
So I'm sorry for the confusion and thank you for the reply!