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Went away for seven weeks. When I came back car was dead and would not accept charging to the main battery. Finally had to get a heavy duty charger for the 12 volt which runs the computer systems. After boosting the 12v the car would finally accept charging to the main battery. Since the big battery usually feeds the 12v I was stuck until I got the 12v boosted. Why did the 12v and the big battery both go to zero in 7 weeks? Is leakage that bad?
 

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Automotive 12v batteries will almost always discharge after a few weeks of non-use. The car used the charge in the main traction battery in an attempt to prevent this, which is why it was discharged as well.

Get a new 12v battery as yours is probably damaged as a result of this deep discharge.

The reason your car wouldn't charge is the computers, including the one in the vehicle charger, are run off the 12V battery - no 12V battery no computers.
 

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How much charge was on the HV battery when you left and how much was on it when you returned? The HV battery normally will not discharge while sitting, at least not very much. And either way even at 0 EV miles the HV battery is far from being fully discharged, the system just won't use it anymore for propulsion until it is charged again.

The HV battery only charges the 12V battery when the car is in READY mode or while the car is being charged. The 12V battery meanwhile is just a standard automotive battery and as obermd said it's not unusual for a 12V battery to be dead after several weeks, especially if the 12V battery is a few years old or if it went through a full discharge sometime in the past. Fortunately nowadays they have those small portable jump start batteries that you can keep in your car, some are so small they fit in the glovebox. They work especially well with hybrids like the Clarity because the portable battery only has to supply enough power to get the 12V system running, then the HV battery will turn the gas engine whenever it needs to be started. And they are safer to use than jumper cables. Even when connected correctly jumper cables can damage the electronics on modern cars.
 

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I had my Clarity PHEV in storage over last winter for about 6 months. Like any car that goes without use for more than a few weeks, I put a maintainer on the 12V battery. When I pulled it out this spring, the main drive battery was still about 2/3 full, which is about where it was when I parked it 6 months before.
 

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Deep discharging a car battery will certainly kill it very quickly.

If you are leaving a car for an extended period, it's wise to have it trickle charged / maintained to avoid having to pay for a new battery out of your pocket.
Plus it avoids having to not have a dead car...

Here's a $25 battery tender:
 

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This was my concern as well. I’m planning to keep my car stored in for the winter and was wondering what is the best way to do that. Obviously trickle charging the 12 Volt battery is number one. Anything else? Thank you in advance for your suggestions.
 

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Went away for seven weeks. When I came back car was dead and would not accept charging to the main battery. Finally had to get a heavy duty charger for the 12 volt which runs the computer systems. After boosting the 12v the car would finally accept charging to the main battery. Since the big battery usually feeds the 12v I was stuck until I got the 12v boosted. Why did the 12v and the big battery both go to zero in 7 weeks? Is leakage that bad?
I left mine plugged in to the outlet for 6 weeks. The 12v battery was dead but not the big battery, it was fully charged. The big battery doesn't charge the 12v battery unless the car is "running". I fixed the problem by setting a climate control turn-on timer for 2 times a week. Problem gone. If your plugged in, great, if not, sorry you'll still go dead.
 

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I left mine plugged in to the outlet for 6 weeks. The 12v battery was dead but not the big battery, it was fully charged. The big battery doesn't charge the 12v battery unless the car is "running". I fixed the problem by setting a climate control turn-on timer for 2 times a week. Problem gone. If your plugged in, great, if not, sorry you'll still go dead.
The 12V battery is also charged whenever the HV battery is being charged. So a similar method to what you are doing is to start with the HV battery at say 30% SOC, and then set a timer schedule of say 15 minutes of charging per day while you are gone, which will also provide 15 minutes of 12V battery charging each day. The advantage is that charge schedule is stored in the car and does not required any outside communication to run. Whereas the climate schedule is stored on the Honda server, and for most people it seems to have intermittent success because communication with the car is not always reliable. So setting a charging schedule is more reliable. And it also does not waste electricity like running climate does. However for a really long time away like the six weeks that you mentioned, you would need to be using level 1 charging instead of level 2 so that you would have more charging time to spread out over all of those days.

Another option is to connect a battery maintainer (like Battery Tender brand) to the 12V battery while away.
 
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