Tag out/appeal play
 

Bases loaded one out. Deep fly ball to centerfield. Runner at 3rd tags properly and scores. Runnner at 2nd does not does not tag and advances to 3rd base. Defensive team appeals to 2nd base long after the run has scored. Umpire calls the runner out who was at 2nd base. Umpires disallow the run. Does the run still count? NFHS Rules. Please provide rule reference and case book reference.

The run counts. This is a time play, not a force out. All codes.

Here's this case play (from an older book, so the numbering might have changed):
9.1.1 SITUATION B: With one out, R1 is on third and R2 is on second base when B4 hits a long fly ball
that is caught by F8. R1 remains in contact with his base but R2 has nearly advanced to third. The throw
to F4 arrives at second base ahead of R2's return. RULING: R2 is out for the third out. If R1 scored before
R2 was retired, the run counts. The inning ended with a play in which the third out was not a force out.

Limacon2,

What did the umpire do with the runner? put him back on third?

Bob is correct run should have counted.

Three outs.

There are now three outs, and the run counts. The answer is the same for NFHS, NCAA, and OBR.