R1 on 3B R2 on 1B
 

Situation for discussion
R1 on 3B, R2 on 1B 1 Out. B3 hits a deep fly to Center. R1 waits on 3B for catch, runs home. R2 thinking there is 2 outs, runs past second before he realizes there is only one out, while retreating to first, he misses second base. The ball is thrown to first base for the tag up put out. The defense also appeals the missed base at second.
Q1 Does the run score? Rule book reference for \ against
Q2 Is the second base retreat retouch miss a defense appeal or can the umpire automatically call him out?

I am interested in hearing your arguements for and against. My partner and I had different perspectives on the proper rules and administration.

Q1. There is never a force when a fly ball is caught. No runner must advance when BR is put out before reaching 1B. So, run scores, no matter how many different appeals are made (unless R1 left 3B early, or missed home), or unless the out is made before R1 crosses (not necessarily touches) home.

Q2. The definition of an appeal is a play that cannot be ruled on until the defense makes the appeal. Unless you do high school softball in South Carolina, that should be self-explanatory.

But what about the issue of R2 having to come back to first to retag? Does this requirement make it a "force"?

No. A force is defined as the requirement that a runner advance because the batter became a batter-runner. The fact that the runner did not tag is not a force; it is a timing play predicated on a live ball appeal.