dead ball balk?

[umpduck11]

Gentlemen,please let me know what you think of the handling of this situation.
Local adult league (38+),R2 steals 3RD,loses helmet,time
is called.Ball is never returned to the pitcher,in order
to attempt a hidden-ball play.
Pitcher steps on rubber,R3 leads off,F5 tags runner.
PU(my partner) calls "Balk".I proceed to go to him,and
discuss the fact that the ball was out into play without
the pitcher being in possession of the ball.Partner nullifies balk call.
Was this the correct action to take by the PU? Nobody
was complaining about the balk,including the offensive
team.Also,was I correct in going to him to let him know
that the ball was previously dead,and could not be put into
play without being on the mound?
Your constructive advice is greatly appreciated.