I don't have any experience in Article III criminal litigation but normally that wouldn't be possible.

The appellate court cannot review something that isn't before it, and a conviction on other offenses does not bring counts 3 and 4 of the indictment before the appellate court.

Normally, I would expect there to be a process for an interlocutory appeal when a ruling is fatal to a charged offense. However, again, I'm not familiar enough with title 28 to say if that is in fact the case here.