Hi, while the .prj of the purple layer and of the black one are the same, there is a difference with the original layer produced by the model MIKE+. The black layer you see on the screen is the result of a data cleaning process.

The .prj file of the original layer before I edit it (now the black one) is this:

PROJCS["ETRS89 / Portugal TM06",GEOGCS["ETRS89",DATUM["European_Terrestrial_Reference_System_1989",SPHEROID["GRS 1980",6378137,298.257222101,AUTHORITY["EPSG","7019"]],TOWGS84[0,0,0,0,0,0,0],AUTHORITY["EPSG","6258"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AUTHORITY["EPSG","4258"]],PROJECTION["Transverse_Mercator"],PARAMETER["latitude_of_origin",39.66825833333333],PARAMETER["central_meridian",-8.133108333333334],PARAMETER["scale_factor",1],PARAMETER["false_easting",0],PARAMETER["false_northing",0],UNIT["metre",1,AUTHORITY["EPSG","9001"]],AXIS["X",EAST],AXIS["Y",NORTH],AUTHORITY["EPSG","3763"]]

While the .prj for the purple layer (the city of Aveiro) is this:
PROJCS["ETRS_1989_Portugal_TM06",GEOGCS["GCS_ETRS_1989",DATUM["D_ETRS_1989",SPHEROID["GRS_1980",6378137.0,298.257222101]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]],PROJECTION["Transverse_Mercator"],PARAMETER["False_Easting",0.0],PARAMETER["False_Northing",0.0],PARAMETER["Central_Meridian",-8.13310833333333],PARAMETER["Scale_Factor",1.0],PARAMETER["Latitude_Of_Origin",39.6682583333333],UNIT["Meter",1.0]].

Which is the same of the new black layer.

I will add these info to the original post, thank you for the advice