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Oops, I misread what you said. I thought that you had flashed TWRP to both recovery and boot. Theoretically flashing boot with boot.img from the update shouldn't be a problem.
It's unfortunate that "boot" is used in different contexts, it breeds confusion. You can "fastboot flash" an image or you can "fastboot boot" an image, they are a bit unrelated. The "gold standard" is writing an image to a partition (using edl, fastboot or adb dd) then doing a reset. I've seen lots of cases (which I couldn't nail down) where "fastboot boot" doesn't start up correctly, probably because of cmdline getting confused? In many cases "fastboot boot" does work and if it does it's an easy way to try out an image without writing anything to flash. If you do hit problems it's worth trying with the "gold standard".
Don't go crazy flashing things. You might be digging yourself a bigger hole.
Some people have had problems where the only thing that changed was the A/B slot somehow. Fastboot can also flip A/B and I would trust that a bit more than the Python EDL. The process involves relabling the GUID type for all the partitions from boot <--> inactive, etc and rewriting structures in /misc. If you have A/B and you wrote some random /misc, that could be the problem. I don't have A/B so I can erase /misc without a problem. Don't you do that!
Did TWRP maybe do an update on you?
You should be able to boot to recovery from EDL. I've never had success booting to fastboot from EDL. It seems to ignore "bootonce-bootloader". Since you have A/B you have to be careful screwing around with /misc. You can pull one "sector" (i.e. 4096 bytes) of misc and then hex edit the very start to read "boot-recovery". Then write it back and tell EDL to reboot.
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