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Hi Andrew,
As I understand it after reading your description, you have completed your ADFS configurations before, and now you just want to replace the old DirSync tool with the new AADConnect tool.
If this is true, then you don’t need to go through the entire ADFS configuration process which is integrated in the AADConnect tool. That process is just for administrators who haven’t deployed the ADFS configuration at all. As you also mentioned, the SSO service is actually working fine now. Therefore, you just need to complete the wizard merely as a synchronization tool, and skip the steps regarding ADFS configuration.
And if I misunderstood anything about the current situation, please feel free to correct me.
Thanks,
Allen