In a situation where the bases are loaded and R1 fails to touch second base after an overthrow, what happens upon appeal?

In the scenario where R1 fails to touch second base after an overthrow with the bases loaded, an appeal play is invoked. When a defensive team appeals that a runner missed a base, and the appeal is upheld, that runner is declared out. In this case, R1 missed second base, thus the action of the appeal results in the out being enforced.

Regarding R3's run, it is important to note that if the runner who is put out (R1) was the one required to touch the base for the run to be valid, then that run does not count. Therefore, R3's run is negated when R1 is called out on the appeal for not touching second base. This leads to a clear understanding that R1 being out affects the count of the run scored by R3. Hence, if R1 is ruled out on the appeal, it results in R3's run not counting.