I'm assuming (not a lawyer) that the actual ballot is what is at play. so that means ballots which have votes for any election - house, senate, president, governor, etc. are either valid or invalid.

So yes, any ballot that is disqualified which has multiple selections would be impacted.

The issue is that a lot of the ballots that are fraudulent don't have down-ballot selections, and so the impact of the other races won't be as prominent as the presidential ballot.