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I can see some major disadvantages to running the port alternator through a battery isolator. What are your opinions?
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I think that battery isolators had their place but that place has been taken over by battery combiners; a.k.a., Automatic Charge Relays (Blue Sea) or Voltage Sensitive Relays (BEP).
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but I am not sure if the charging rate will be too high for the AGMs
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AGMs can be charged to their capacity or higher. Charging current is not the problem; higher voltage than the battery manufacturer's spec is.
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Would the diode reduce amperage transferred?
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No, using a battery isolator will reduce the voltage and you will chronically undercharge the AGMs.
When running multiple charging sources simultaneously one of the sources is going to predominate the others and you won't know until you do a trial and error. My guess is that the Pronautic with its sophisticated charging algorithm will dominate the internally regulated alternator on the house side and the ProTech will dominate the port alternator on the starting bank.