I have an ArcGIS service into my Portal (10.3), also I have an script that replace directly into the database where those files are stored.
The problem is that when I run the script I see a blend of the past last layer with the new layer.
The output is
output = "C:/arcgisserver/directories/arcgissystem/arcgisinput/pronosticos/pronosticos_db.MapServer/extracted/v101/pronosticos.gdb"
The replacement is made with a simple clic
arcpy.Clip_analysis("gfs_precip_gis_48_"+ date + ".shp", clip, output + "/precipitacion_48horas")
Also I set
arcpy.env.overwriteOutput = True