Hi Darren,
Can you please let us know how do you set up the second ADFS server for the sub domain?
Generally, when we convert a top level domain to federated in Office 365, the sub domain will be converted to federated automatically and all the sign in requests will be redirected to the ADFS server where the top level domain is set up, and we don’t need to set up additional ADFS server specifically for the sub domain.
Also, since federating a sub domain into an existing ADFS farm is an issue related to the on-premises servers part, which currently our forum doesn’t focus on it, to ensure you get dedicated support about the on-premises server settings part, it’s recommended that you post a new thread with details in our Windows ADFS Forum. Your understanding is appreciated.
Our community members who have run into the similar situation before are welcome to share their experiences about the scenario, so that we can benifit from each other.