Generally, the source code is only required for verification whether the game was actually made in GM:S 2 and doesn't need to be made public. Quoting this post:
> QUESTION: Can you clarify the situation regarding providing source code please @rmanthorp? You said you were sure it wouldn't be public, but haven't actually confirmed this, nor - if it's NOT public - what we'll have to do to let YYG see it.
> ANSWER: Yes. Not public. Anything you don't want to share don't share and when it comes to judging/confirmation we will reach out privately if we require proof of GMS2.
Since the main purpose of the source is verification that the game was made in GM:S 2 - and considering the fact that it doesn't need to be made public in the first place - I think you should be fine.
To be on the safe side, you might want to replace all the paid sound assets with silence (removing sound assets altogether could break things) and explain the situation to YoYo Games (while keeping the original to yourself). I'm sure they'll understand.