I can't believe doing an update twice would have this effect. That's like flashing a rom and then flashing it again and bricking it. In the Root world of android, this is done all the time. Something is not coded correctly and that is what's causing the problem. Doing a flash twice should not do this.
Given the size of the patch (22 or so Mb) this is not like flashing a rom. It's more like applying a context binary diff. It seems that this is not an idempotent process (most patch tools are). I'm kind of shocked that they would deploy and upgrade tool that never bothered to check this. And even more shocked that the OTA version check doesn't exist or doesn't work.
This is 20 year old technology and standard operating procedure for OTA upgrade systems.
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