So I made a mistake and forgot to test my game after deployment.

Apparently the options I had selected deleted some of the assets necessary to run the game.
Is it possible for me to fix that?

Unfortunately, at this point, your best bet is to hope that the judges can at least play enough of your game to make it past screening at least.

I had that happen last year and almost again this year! That is a very dangerous button to hit. It does hurt and hopefully you can get passed screening if not it's something to remember for next year to always check before submitting.

Yeah, RPG Maker MV's delete unused files doesn't take into account stuff that's used for plugins. I went through my project and manually removed the RTP stuff I didn't need (even then I didn't dare touch the sound effects or battle animations just in case).

There is a workaround for the plugins issue where you basically force them into the game with a common event that you never call, but contains every asset used by the plugins.