If all lamp extinguish simultaneously, they are all being fed by the same branch circuit of the power distribution. Investigate the wiring of that circuit in the portion that is common to all those lamps. Investigate both the positive and negative branches of the circuit.
Also, are you certain that no other electrical loads are affected? That only these lighting circuits blink? The reason I ask this: it is unlikely that the navigation lamp circuit is part of the switch illumination circuits of other switches. If ALL the switch illumination lamps extinguish in unison with all the navigation lamps, then the cause is probably not in either individual circuit, but in a common circuit that supplies power to both branch circuits.
Generally the power distribution wiring on a small boat is confined to a very limited area, and a visual inspection of the wiring can easily deduce how the circuits are arranged. Since it is impossible for me to make a visual inspection of the wiring of your boat, I cannot offer any advice on how it might be wired. That investigation will have to be done by someone who can see the wiring.
Have you obtained an electrical wiring diagram from the boat builder? Boston Whaler generally provides on-line resources that include electrical wiring diagrams. You can often find PDF versions of engineering drawings at
https://www.bostonwhaler.com/boat-ownership/resources/I don't see a wiring diagram for your model and model year. Here is a diagram for a similar model and slightly newer:
http://bostonwhaler.com.s3.amazonaws.co ... m-2007.pdfThat diagram may be useful or at a minimum will give you an idea of the typical circuitry used by Boston Whaler.
If the electrical wiring diagram is not available on-line, you can contact Boston Whaler. Boston Whaler is renown for their excellent customer service department.
Once you have a schematic diagram of the electrical wiring, the arrangement of the branch circuits in the power distribution will be clear. Concentrate on the circuitry that is common to all the lighting loads you have observed blinking.
Also, is this boat operated in saltwater? Is would be quite common for electrical connections on a boat that has been operated in saltwater for almost 20-years to develop corrosion, particularly at any point where a connection is made that is exposed to air. In 12-Volt circuits, even a very slight corrosion between electrical contacts can be sufficient to stop the flow of electrical current.
A general approach to solving this problem may be to obtain a spray can of WD40 with a tube in the nozzle. Without using an excessive amount, spray any suspected electrical contact with WD40. Undo the mechanical connection of the electrical conductors to each other. Re-make any plug-socket connection. Re-tighten any connections made under a screw fastener.
The preferred method to investigate this problem would be to pinpoint the one circuit that is causing all problems. You should be able to do that by slowly and carefully manipulating just one conductor at a time, while observing the behavior of the lamps that are affected. In this way you will know when you have found the real source of this problem, and they you can be certain you have remedied the problem. Locating intermittent electrical problems can be very time consuming. Investigating this yourself will be the best method, as paying a skilled technician an hourly rate could be an expensive solution.
HINT: inspect a large conductor, probably red 8-AWG that originates at the main circuit breaker (positive) and provides power to ALL switches, their loads, and their illumination. Also check the negative portion of this circuit.