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Ah! I found the issue. It turns out that some of the attributes are read-only so I would be able to put the entire instance back again and that is where it was failing. I have changed it so it is now just updating the attribute SSLCertificateSHA1Hash.
Set-CimInstance -CimInstance $RDPInstance -Property @{SSLCertificateSHA1Hash=$Thumbprint} -PassThru
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I didn't managet to do this by modifying the .rdp. But a workaround is, to change the settings of the remote desktop connection application. In Preferences -> User Accounts you can add your account + password:
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