I am an Indiana lawyer. There is no hard and fast rule about leaving your children in the car. But I can tell you that people are arrested for child neglect all the time for leaving kids in the car. A couple years ago a doctor in Indiana was arrested for child neglect for leaving her toddler in the care while she ran into a store: http://www.courierpress.com/news/2008/jan/03/couple-accused-neglect-appear-court/
Your course of action here would be to challenge the citation issued by the HOA in court. You can request and administrative review of the citation or just refuse to pay it and challenge the legality of the rule in court.
As I have mentioned, there is no established "law" on this exact issue. So you would have to seek a ruling by challenging it. Personally, I think you would have a good chance of winning.
Yes, my answer is still to ask for a ruling from a judge. There is no defined law on the issue in Indiana that you can just present as a definitive end to the discussion. It is a balancing test as to whether the harm to you (having to wake your kids up) outweighs the benefit to the neighborhood.
You can send them an email explaining the situation, but there really is no relevant law or case that would support your position.
At this point it is a matter of negotiation with the HOA. You can seek a pre-emptive ruling from a judge stating how he will interpret the law in this case.
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