UPDATE: I managed to delete all the 'wrong' baseboards. It was a good hour of constantly deleting. Got rid of around 180 baseboards. Now I have a clean standalone Electro Island v 2.0. ready for re-merge with a hopefully 'clean' Landbridge map. Thanks for the help. I also backup the standalone versions now of both routes.
As a bonus the maps will be more optimized because I also got rid of a lot of unused tiles.
As a bonus the maps will be more optimized because I also got rid of a lot of unused tiles.