That's interesting because toggling Safari off should only affect Safari.
I'm curious, are you following this path: Settings > Screen Time > Content & Privacy Restrictions > Allowed Apps > Safari ?
I have seen people change the age level of Apps to lower than 17+ and that will affect Covenant Eyes. If you lowered that setting go back and raise it to 17+: Settings > Screen Time > Content & Privacy Restrictions > Content Restrictions > Apps > 17+. Once you do so, Covenant Eyes should reappear.
If both of those items check out ok, and Covenant Eyes is still gone, then there is some other, uncommon, factor in this equation. At that point, I'd encourage you to contact Customer Support via live chat (the blue speech bubble in the lower right-hand corner of My Account) or phone (+1.989.720.8000).