Sounds like you had a dead cell in the battery and now resolved I hope.
I have had no issues with the battery charge amount after making sure I drive with the headlights on to get over the Honda ECU control circuit. I did try the disconnect battery and short out the battery leads so that the ecu and car rebooted (causes the radio to check if correct) I saw the charging system work OK on the short first drive until I restarted the car and it went back to not charging correctly.
I have seen thoughts of using the rear heated screen and mirrors to get the battery charged but they are on a timer.
I'm not worried about the stop/start not working but still seeking a method to resolve this problem.
Avoid the RAC as they don't reply to resolving problems and now have a bad list of reviews if you search.
Marnoch (Min) G0JMS
Faults and Technical chat for the Honda HR-V