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Have you ever received an alarm for the center engine?
does it run warmer than the other two?
Switching the batteries off before the motors can cause all sort of alarms, provided it happened right after the switch was turned off. It is really odd that when in sync, the middle engine will cut out. That is sounding more like it is the control handle with the sync more than anything else.
A certified Verado tech with the CDS can recalibrate the throttle handles and see if the issue will be resolved by that. If that does not take care of it, the handles may need to be replaced and you may be able to get Mercury to cover part of the cost, as this is a safety issue with the boat. There have been a few handle issues in the past, but I do not recall one like this.
CDS is the Computer diagnostic System that Mercury dealers have to talk to the Verado engine and its components. They may help as this is a safety concern for your boat.
Take the engine serial number and the boat serial number to a Mercury dealer and ask them to look it up on MercNet. That is the dealer network where Mercury puts out all of the bulletins.
That stinks. Did they give you a time when they may be able to adapt the handles again?
Two weeks out is not that bad for this time of year. I really think that there is something amiss with the throttle. Perhaps when they scan the command modules, they will locate a fault there.
I wish that I could do more on my end.