Fellas let's use Edison and Lilith as an example here
Edison orders the Seraphim to kill Kaku, Lilith can not override the order as they're on the same authority level
The Seraphim blow Kaku's giraffe brains out, they have confirmed the kill and completed their order
As they have completed their order and killed Kaku they're now in a state where Lilith can give them an order again as it is not overriding the order that Edison gave them.
Apply it to the "Stop Fighting Now" command, they were fighting and ordered to stop. As they have completed their order and stopped fighting they're now in a state where another Vegapunk can follow-up with an order of their own.
If this was not the case then a single quick order like "shake my hand" would mean that vegapunk has control over the Seraphim indefinitely which is counter-intuitive to the hierarchy. Edison gives the shake my hand command and goes off somewhere seperate and now the other vegapunks or below can not access the Seraphim until he comes back.
So just because Edison gave the "stop fighting" command does not mean he is still in control and the other Vegapunks (or others) can't order the seraphim. Especially if he ends up being accounted for in one of the groups when the seraphim are given the order to attack