When switching between GGGL E and VRTL E should I run the clean up.bat before switching services in the .ini or is it ok just to do the switch and carry on?

If you intend to fly at a spot that you have been before, expect a mixture of textures between GE and VE to appear. So in this case, cleanup helps clearing up the tile mishmash.If you intend to switch locations as well, everything is fine.