2017 Grand Cherokee Battery w. aux S/S

Have 2017 Grand Cherokee with Start/Stop system.
Yesterday would not start.
Both batteries were drained. Auxiliary battery for start/stop at <5V
Main battery <11V.
Charged both AGM batteries with AGM battery charger. Ran vehicle that day.
Next AM both batteries at low 12V. Had to charge both again.
Autozone tested charging system, advising ok
After charging main battery tested OK, was advised their tester can't test the auxiliary one.
I am suspecting the main battery being bad and not holding the charge. Will a bad Main also drain the auxiliary?
Do I charge both, disconnect and test battery voltage next day?
Do AGM batteries behave different than Lead/Acids ones?

1 year old. Warranty work at dealer.

Long distance commuter. Jeep has over 100K miles in almost 2 yrs. MFG warranty long gone.
Either way, did take it in to dealer. Short in fuse box.