In order for water to be completely terraformed you need to use Clear Natural Water Status/Depth from debug actions menu. This function is of course currently buggy and you will be able to remove status from one tile at a time. To use it first left click in whatever place then left click on a tile you want to remove status from, it now starts to draw rectangle but the status will be removed
only from the first tile (propably!) so again left click somewhare and then right click to conclude operation.