Catalina 350 International Association

Would very much appreciate the expertise of you guys on this forum regarding this issue.
I will dig deep into this but a little fore running with you would be helpful.
For context we have a house bank of 3 Firefly foam core installed 2017 and a 2 month old starter battery,
a Balmar 100A alternator just rebuilt, a Balmar ARS-5 voltage regulator, Xantrex Link 1000 / Heat Interface Freedom Inverter Charger and a brand new Blue Sea SI-ACR. Plus we have an Efoy fuel cell generator. Fully charged on shore power they float at 13.20 and unplugged and just underway they read 12.70
Here what happened - 3 nights at anchor and two full days without running the engine ... we did not run much load - frig, water pump, electric toilet etc and shut the frig off toward day 3. We did run the Efoy a day or so but shut it off as we had no reason to suspect a problem. Nothing on the Xantrex that gave me any concern.
Leaving that location the engine cranked twice where normally it fires instantly (first indicator something was up) Primarily motored eight hours and anchored again for night 4. We used very little load, no frig, some windless, as we were leaving in the am under power.
Next day the starter battery was down to 8.5 and couldn't crank once. I jumped the starter battery off the house bank and started up right away. Another 8 hours of motoring 2300 rpm I watched the voltage on both banks carefully all day, cushions all off with a multi meter. Suspecting something was not right I ran the Efoy all day and house came up a little 12.5 - 12.10 VDC. I suspected the Efoy was doing something here and suspect we are getting nothing from the alternator. Or ??
The starter battery however dropped consistently to 1 and then .05 VDC. All gauges went to zero and the ARS-5 LED display went blank.
I have watched this display before and noted the only new error code was 24 - Voltage Reg exceeds 90 degrees C.
We found a marina that night and plugged in fully expecting the starter battery to be toast as well as the voltage regulator.
Several hours later plugged in house bank looked ok but the starter hadn't budged which sort of confirmed my suspicions.
I realize the ACR has a low voltage lock out which was flashing. Flashing all day for that matter.
Well - in the am getting all set to jump again both banks were fully charged and floating at 13.2 VDC!
ACR was indicating combined charging and all was normal again. Fired right up and all gauges working properly.
Back at home port plugged in and all is normal but, of course, it is not.
Any thoughts / advice?
One last note for context. We sort of had this issue 2 weeks prior but not as dramatic which lead to suspecting the alternator which indeed needed rebuilding and the installation of an ACR. After installing the ACR I set the battery selector switch at 2 which is the house bank (as advised)

Thank-you in advance

Sounds like two separate systems are not charging:

Not familiar with an Efoy. Looks like a 12VDC charger. If so, doesn't sound like it is working. Pretty easy to verify with digital voltmeter: Voltage at the battery before starting it and after.

And, those voltages while motoring are way low. Your high output alternator and smart regulator should be starting (bulk rate) over 14 VDC as soon as amp load is below full output of the alternator.

I would start by going though the troubleshooting for the Balmar ARS-5 voltage regulator. That will test regulator and alternator. If you need help, call Balmar. They have some knowledgeable techs.

The only charging system that appears to be working is your Freedom inverter/charger.

You need to troubleshoot both Efoy and alternator/regulator systems separately.

And, long crank time to start with low voltage could be explained by glow plug not properly pre-heating the engine and starter RPM lower at lower voltage.

Thank you Brett. I appreciate this.
Time to dig into it.

A quick follow up on this issue I posted previously.
I found the problem. It was the inline 135A Thermal Breaker between the alternator and the pos bus - house bank.
I went through all of Balmar's trouble shooting and Nigel's, which was a great exercise in better understanding this circuit.
I would reiterate part of Brett's very helpful advise in that you should CALL Balmar. The technical department is excellent.
Balmar is excellent equipment but the manuals can be scant in some areas.
For example the ARS-5 troubleshooting test on the field wire states you should see a voltage between 4 and 11 VDC.
What they don't put in print and I learned by discussing my results with them is that if this is an instant read of 11, there is a problem but if
it ramps up to this voltage over the course of approx. 1 minute (or the highest you get), then that indicated no problem in that area.