Just tested the reset of globals.gd when simply applying mod again(easy to test by simply adding anything to the file). There were no problems and the file was restored to original before the mod was applied.
Edit: Though I have seen cases where the mod system had an error while changing globals.gd when applying a mod and the file was not completely changed. This would not be changed by an additional reset. Only applying a mod that doesn't conflict with the mod system can fix that.