This has never happened to me before but at least I know how to handle it now
This is a high school match using NHFS rules.
I am R1 and blow the whistle for serve. The server is the Libero who rotated into that spot. The Libero notices that the two middles never exchanged. Libero is trying to get her coaches attention and finally does. I am at 4 on the five second count and the coach yells for time out. The R2 grants the time out. All the players leave the court. I yell to my partner that there is no time out because I blew the whistle for serve. He apologizes and says he did not hear my whistle. We get all the players on the court. This entire exchange took about 30 seconds. After all the players get back on the court, coach makes correct Libero replacement with the two middles. We let the exchange happen because of inadvertent whistle and replay. Clearly we were wrong
Oh well, chalk that one up to lesson learned. The oddity to me is that only the server and I heard my whistle I guess as the coach and R2 did not hear it. I know I blew the whistle loudly and to the same level as I had the entire match.