I'd agree with Christoffer. Given the physical topology, there seems to be no compelling reason to have domain-level different replication scopes
Getting there might be a bit challenging giving your current situation. My suggestion would be to:
- configure the root domain DCs functioning as DNS servers as secondaries for both child domain DNS zones
- once that's completed, point all DCs to a single DC in the root domain
- restart the Netlogon service and run ipconfig /registerdns on all domain controllers
- wait a bit and check the replication/health again
- assuming that the situation stabilizes, modify the scope of replication to forest-wide for both child DNS zones
- reconfigure DNS settings so each DC points to itself and at least one another DC as the resolver
hth
Marcin
