B1 is taken out of the game for a pinch runner. (Not the pitcher or catcher, so no courtesy runner). She later returns to bat and receives a walk. She was never reported as a re-entry. Umpire rules B1 out and also DQs her as an illegal substitution. After the game ends, B1s coach protests the game saying that B1 should have been out, but should not have been DQd.
Q1: What's the correct call?
Q2: Can the protest be filed after the game?
ASA and Fed if they are different please.