No, it won't.
If you want to remove the waygate sound then you can always just import a blank sound with the path of the waygate sound.
Just make some blank sound (record one, or find one on the internet, or just trim a sound to have a duration of like 0.1 seconds or something). Then import it and put it under whatever path the waygate sound has. Sorry that I can't be more specific, I hope this makes sense.