I’m not sure I understand what you’re saying.

There is a domain abc for which DNS requests shall be sent to an upstream DNS server on the VPN and there is another domain xyz for which traffic must not go over VPN.
These are two rules that should be pretty independent from one another. I don’t see why preventing traffic for domain xyz go over VPN should interfere with name resolution for domain abc being forwarded to a specific DNS server on the VPN.