That is why bases loaded or 2 runners on (any base) with one out is a time play. The PU has to stay home, BU has all the bases.
On a break-down play that ends up an inning-ending double play, R2 may be a close one. That run may determine the game. We, as umpires, should try very hard to get this concept right.
The appeal 3rd out, or in the rare 4th out case, erases runs scored AFTER that runner, not runners AHEAD of the successfully appealed runner.