Freix,
You do bring up a valid piont that the Base Umpire, stationed inside the diamond would likely not see the earliy movements of the infielders - in your situation, a lateral movement of F6 away from the ball to create a collision.
And I would say "Yes," it is at this time that you need to come to his rescue. Fans, players, and your partner would understand if you can matter-of-factly plead your case that the call needs to be changed because your partner did not see this initial motion - the fans and the players in the dugouts likely did see it. I don't believe it will take great effort to help your partner realize that this call needs to be gotten right and possibly changed.
An immediate dead ball, some pointing to location of the ball, location of the contact, pointing towards culprit and victim. Everyone is going to get the picture. There may be some screaming when the call is changed but if you don't get it right, I would guess that this kind of contact once allowed will lead to greater and more potentially severe contact in retaliation... and potential player injuries or fighting.
It is during the most difficult times that the players and fans really need to know that you are in charge and not just making ball and strike calls.
