Upgrading to 2.4.6-r2 removes the /etc/ssl/postfix directory. I was able to resolve this by reemerging postfix-2.4.6-r2 a second time which recreated the directory and keys. Reproducible: Always
That's a result of fixing Bug 174759/Bug 201671 and unfortunately nothing that could be fixed without overwriting people's certificates unconditionally which sucks.