I tested with a pure OVN cluster which is not migrated from openshift-sdn. I can see similar symptoms. Rebooting all nodes at the same time made the ovn-kubernetes pods not working. So I think it is a problem of the ovn-kubernetes itself, not the migration.
It might be releated to https://bugzilla.redhat.com/show_bug.cgi?id=1858712
@pliu can you update the status of this please? Are there any other PRs needed other than the two now linked? I know you have a hold on one waiting for another PR to merge (https://github.com/openshift/machine-config-operator/pull/2085)
Since the problem described in this bug report should be resolved in a recent advisory, it has been closed with a resolution of ERRATA. For information on the advisory (OpenShift Container Platform 4.6 GA Images), and where to find the updated files, follow the link below. If the solution does not work for you, open a new bug report. https://access.redhat.com/errata/RHBA-2020:4196