Hi Ev,
Based on the error message, the issue should be caused by the reason that multiple federated domain cannot be hosted on ADFS 2.0. To resolve the issue, please refer to the following steps:
1. Install Update Rollup 1 for AD FS 2.0 on the ADFS server. You can refer to the following article to get the download link:
http://support.microsoft.com/kb/2607496
As a tip, please restart the ADFS server after you install the update although you may not be prompted to restart the computer.
2. Run the cmdlet Convert-MsolDomainToStandard to convert the current federated domain (here is rootsuba.co.uk) back to a standard domain. Here is an example:
Convert-MsolDomainToStandard -DomainName rootsuba.co.uk -SkipUserConversion $false -PasswordFile C:\temppassword.txt
3. Run the cmdlet Convert-MsolDomainToFederated to convert the custom domain to a federated domain with the -SupportMultipleDomain parameter. Here is an example:
Convert-MsolDomainToFederated -DomainName rootsuba.co.uk -SupportMultipleDomain
4. Use the same cmdlet to convert the second sub-domain with the -SupportMultipleDomain parameter too.
As a tip, in this case, please make sure that the second sub-domain has been verified with your Office 365 tenant before you run the cmdlet. Moreover, since we need to convert the current federated domain to a standard domain temporarily, I suggest doing this change in a non-park time, such as weekend, to avoid a short period of down time.
As for your concerns, you don’t need to re-run the ADFS Configuration Wizard again or configure another ADFS server deployment.
Thanks,
Claud
