Testing confirms that doing so wiped the points, and also likely caused a clouds issue that I just encoutered. Who knows what else.
Anything to do with the 'state' table (basically any 'extra' information included in the saved game via lua events) will have been removed.
Since you will be using the cheat mode anyway, it might be easier to use the civ.deleteCity, civ.addImprovement, and civ.removeImprovement functions through the console to delete the extra cities and give the correct improvements, rather than messing about with the events.lua itself.