Currently there is no way to "refresh" a standard Layout object using the mp module. You can however refresh a mapseries.
import arcpy.mp as mp
# Current behavior for mapseries
project = mp.ArcGISProject("CURRENT")
layout = project.listLayouts()[0]
layout.mapSeries.refresh()
# Desired behavior for layouts
project = mp.ArcGISProject("CURRENT")
layout = project.listLayouts()[0]
layout.refresh()