Ruling: If after the umpires get together and agree this fly ball met the criteria of Rule 1, INFIELD FLY, and the umpire failed to make the correct call at the time, then Rule 9, Section 1A[1-4] allows the umpire to call “Infield Fly” when the opposing team brought this to the attention of the umpires. In regards to R1 at 3B, by the umpire not calling “Infield Fly” this put both teams in jeopardy. Rule 10, Section 3C allows for the umpire to rectify any situation in which a reversal of an umpire’s decision or delayed call places the offensive or defensive team in jeopardy. In the above case, the batter should be ruled out for Infield Fly and return R1 to 3B.
As to the question of whether the umpires can decide, after the fact, to call an Infield Fly or not, the following information should be noted:

1) If the umpires thought it was a fly ball that could be caught by normal effort (Rule 1 Definition Infield Fly) and did not call infield fly, then the opposing team could protest a misapplication of the playing rules under Rule 9A, Section 1-4.

2) Not calling infield fly put both the offense and defense in jeopardy, especially the runner from 3B attempting to score.

3) Rule 10 Section 3C allows the umpires to rectify any situation in which a reversal of an umpire’s decision or delayed call by an umpire places a batter-runner, runner or defensive team in jeopardy.

In this case, if the umpires decide, under protest, that the Infield Fly Rule should have been called, then they put the defense in jeopardy by not knowing that they had to tag the runner. The umpires should have returned all runners to the last base touched before they ruled the batter–runner out on the Infield fly rule that should have been called.