Did you find a solution?
I am also looking for a way to do a bit-for-bit copy of the SD card on my Raspberry Pi running hass.io.
My backup procedure for all of my Raspberries running Raspian (Jessie and Stretch) is to simply go to “Accessories”, “SD Card Copier” and make a copy of the boot SD card. But it won’t copy the SD card if the source is a hass.io image.
Short answer, no, you don’t have to shut HA down. I use exactly this approach on my venv based install. Mind you, if you’re still on Python 3.4 then you’re running a very very out of date system
For imaging a Hass.io based build, you would have to shut it down first as you need to pull the SD card, and then there are many tools, including dd that can be used to image it.
I have updated my system to Python 3.6 since I posted this message.
RPi-Clone runs without any issues, but I don’t remember if it did before the upgrade as well already.
It also takes hours for it to complete my 64GB card, but at least it runs ‘in the background’ so the HA functionality is not impacted much - I still trigger it manually, though.
Triggering manually IMO is the right thing, because you’re over-writing your config. I do it a few days after a successful upgrade, so that I’ve always got the ability to boot to a known solid system.