I don’t have an AIY kit, so just ventilating some ideas here;
sudo apt-get -y install aiy-python-wheels
Isn’t this command perhaps change the /etc/pip.conf to add/remove/change the location of where to get wheels from? I believe the picroft image has added the piwheels repository
And the protobuf package is there;
You can change / override certain things via /etc/pip.conf (https://pip.pypa.io/en/stable/user_guide/) perhaps a (quick) fix lies in changing the config file to grab that certain protobuf-3.6.1 package from piwheels instead (forcing it baqck if aiy-wheels had changed it)
quote from the pip manual; “Command line options have precedence over environment variables, which have precedence over the config file.”
So perhaps something like thius will work;
pip install --find-links=https://www.piwheels.org/simple/protobuf/ -r requirements.txt
Again, no AIY here, so just sucking some stuff out of my big thumb. To me it looks like the debian package; aiy-wheels install some preset wheels or wheel location overriding the one configured from piwheels in /et/pip/conf
Forcing it back, or somehow blacklist the protobuf again might fix it.
Hence, perhaps protobuf was not yet included within the aiy-wheels debian package before and they did now in the last update.