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Seems some of your question didn't make it on to me? Problems with the charging system?
While I am waiting I will caution you not to disconnect the battery while it's running. The voltage surge(spike) it creates can fry the engine computer plus any other electronic control module(there are many). It was a old school test before electronics a very long time ago.
So what is happening? All I got from you was: new battery .disconnect battery when car is running it doesn't stall. 09 Pilot.