Overwriting features without first removing their layer using ArcPy

I’m currently using arcpy.env.overwriteOutput = True because I want to be able to play around with variables and not have to delete the file from my gdb every time. But whenever I rerun the script with a changed variable it runs fully but then my changes were not implemented even if I drag the feature back onto my map.

I found the only way to get it to overwrite is to delete the layer from the dataframe first (see image) then run script and then it appears with my changes.

Is there a way around this?