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I inherited a migration of ADFS 2.0 on Windows Server 2008R2 to ADFS on Windows Server 2016. The task had been started manually, but not completed. I am using the MS scripts, and exported configuration via Export-FederationConfiguration.ps1. The warning stated that I ensure I used a specific service account on the target server. However, upon verification, the ADFS 2016 service account is not the same user and domain as the source.

Is this an issue? What can one do to correctly import using the import script?

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When you say that the ADFS 2016 service account is not the same user and domain, do you mean that both ADFS farms are on different domains? If that's the case, trying to restore the ADFS2.0 farm to the 2016 farm doesn't make sense because the identity stores would not match.

I would recommend you to treat each ADFS Farm as a unique farm, and recreate all of your relying party trusts and claim rules manually in the 2016 farm.

Are your 2016 ADFS servers in the same domain as the ADFS 2.0 farm? If so, I would recomend you to reconfigure your ADFS2016 farm to use the same service account you have in the 2.0 ADFS servers.

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