Still trying to reproduce the conditions however it appears that our IPv4 root hints have been removed and in place have been only IPv6. We have 1 IPv6 enabled domain controller while the others only had link local, default IPv6 configuration.
Eventually, the IPv4 root hints are gone and we are left with only IPv6. Restarting the DNS service did not fix it and clicking resolve on the record did not bring them back. I had to manually re-enter or copy them from a server that only had the IPv4.
Why is this happening? I have heard there is a bug that was introduced in January 2018 with this issue that affects both server 2012/R2 and 2016 but I cannot find any official documentation from Microsoft on this behavior. Any info?