Hey there, and thanks for replying. In this case, the judges would have discretion as to whether or not they want to count only one play-through. If they decide that, then yes, it would be a problem. My recommendation, to make 100% sure, is to make sure that one play-through lasts roughly 20 minutes.
Also, consider putting a disclaimer at the start of a new game stating what you just said. That should also help work in your favor. Think of it this way, the more information a judge has on your game, the better.
I hope this helps. Unfortunately, each judge is going to approach things differently.