Succinctly, replays indicate that as R1 held between first and second base and Ole Miss RF Treyson Hughes ranged over to catch the batted ball, the first base umpire, having run into the outfield to officiate the fly ball, signaled "safe" as in "no catch". Thus when R1 cruised into second base and stayed there, only to be tagged and appealed-on, Namoa responded by pointing to the umpire and indicating the erroneous "safe" mechanic.
NCAA/college's rulebook holds two outcomes for getting the call right in Appendix E—one for crew consultations without video review, and one for video review calls.
Both scenarios play out similarly in terms of correcting an erroneous initial call: "If the reversing of a call results in the need for decisions on the placement of base runners, the umpire crew shall use their best judgment to determine their locations as if the call had been made correctly."
OBR 8.02(c) is similar: "If the umpires consult after a play and change a call that had been made, then they have the authority to take all steps that they may deem necessary, in their discretion, to eliminate the results and consequences of the earlier call that they are reversing, including placing runners where they think those runners would have been after the play," while NFHS 10-2-l/high school grants umpires-in-chief the authority to "rectify any situation in which an umpire's decision that was reversed has placed either team at a disadvantage."
The general principle here is that no player shall be placed in jeopardy because they relied on an umpire's incorrect initial call. Accordingly, R1 was returned to first base and the batter declared out, the crew deeming via review that had U1 called the batter out initially, R1 would have most likely returned to first base safely.
As a footnote, what may have contributed to U1's error was the right fielder's glove, which was white or grey in color, similar to the baseball's hue. Although NCAA rules do not restrict non-pitcher fielders in their glove color, OBR 3.07(a) states that "no fielder regardless of position may use a fielding glove that falls within a PANTONE color set lighter than the current 14-series." This applies to most white and grey colored gloves and, had this occurred during a professional game, would likely apply here as well.
Video as follows:
Video as follows: