confusion onbases

[bbman]

Had a situation that I had today, it all worked out, but what if???
Runner on first, no outs. B2 hits a fly liner to F9 that looks like it was trapped. Plate ump calls trapped ball, R1 arrives safely at second, B1 safe at first. F9 (thinking she caught the ball), fires to F3 to double up R1 at first. "Time out". Defensive coach comes out, wants to challenge the call. Umps get together and base ump tells plate ump, 'you blew it, she caught the ball on the fly.'
Now what? We want to fix it & make it right.
Do we call batter out & put R1 back on first?
Thanks