Runner misses a base, how many runs score?

[Legacy Zebra]

I am not a softball guy, so bear with me.

Runners on 1st and 2nd, 2 out. The batter hits one in the right field corner and all 3 players end up coming all the way around. After all 3 have touched the plate, the defense appeals that the runner originally on 1st missed 2nd base and the runner is called out.

Obviously that runner's run does not count and she is the third out of the inning. The lead runner's run counts though, right? Appeals are timing plays, not forces, so as long as the runner scored before the appeal the run counts?

What about the BR? She scored before the appeal, but I seem to recall reading somewhere (maybe even on this board) that no succeeding runner can score if an appeal is the third out. Or maybe I'm just crazy and made that up.

I'm interested in answers from any and all codes.