Here’s how to replace a self-signed Exchange certificate in the Exchange Shell.
First get the list with details:
Get-ExchangeCertificate | fl
You’ll see all of the certs, with expiration dates (“NotAfter”) and thumbprints. For each one that you need to replace, do this:
Get-ExchangeCertificate -thumbprint <thumbprintcontents> | New-ExchangeCertificate
Then say Yes.