Glad you had a provision to get you back on the road, and back on your trip! Seriously, it was a good save.
With any failure, it's always worthwhile to ask what got you there. You might not like what you're going to hear, but I highly suspect the following that led to your failure. Please correct me if any of my assumptions are wrong, as I haven't looked at your setup in detail.
I believe you said you have an AGM house battery and flooded starter batt. An isolator that disconnects the banks upon stopping the vehicle. They link together to charge when the vehicle is on.
Battery setup 101 tells us to never mix battery types. Yes, you have an isolator to separate under discharge. In charging, it's just as important. Mixing batts of the same type even if they differ in capacity, is somewhat okay. Mixing different battery types is bad.
What led to your flooded starter batt prematurely failing is that it had been systemically undercharged.
Because of the mixed battery type.
AGMs have less internal resistance, and can charge and discharge quicker. When the vehicle is on, two things are likely going on:
- AGM, due to less internal resistance, is taking majority of the current to charge first
- Once AGM is full, the regulator senses reduced load on the electrical system, reducing its output, causing the flooded never to fully charge.
Exacerbating this perhaps is the AGM has better standby leakage qualities and you may not be regularly using house accessories. When starting the vehicle and the isolator closes, the alternator/regulator senses full just about immediately and never putts charge back into the flooded starter batt.
Flooded batts hate being undercharged and will sulfate. Sulfate sheds collect as piles underneath the battery plates. When enough of this happens, and potentially with the long drive the day prior, winds up shorting the cells such that it will never have a chance to produce 12V again.
Shorted cells happen, but it is not the normal failure mode of a battery in a well designed system. As you found out, cannot support a running vehicle. Batts generally fail in the manner of holding less charge, and in this failure mode, a jumper can help a car run with a compromised battery.
In regards to your side note. The AGM is full and reads higher. The flooded batt is drawing the voltage down either because of an internal load or short. What does it read without any charging?
I believe you can fix your setup with a common battery type. Otherwise, this may well occur again.