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The question comes down to how the neonode chip works & communicates, and whether there is another way they can force it to shut down, if my conjecture is even correct. I really need to find and read that neonode chip's data sheet.
Another possibility might be to shut the unit down manually by flicking the switch while the cover is still open in order to provide time for the neonode to shut down prior to closing the cover, and just run the code to check for the absence of the magnet to wake it back up as long as that option was turned on in the settings. I really just think it comes down to a timing issue where you need to make sure it's shut all the way down before anything gets a chance to block the IR.
A far simpler solution is to make sure there is nothing floppy to block the IR. A bit of crazy glue or a stitch or two might solve the problem...
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