Will this change have any negative effects on end users such as their consents will be invalidated and they will have to reauthenticate?

This depends on how the certificate will be issued. We take the OrganizationIdentifierOID=2.5.4.97 / organizationIdentifier from the certificate to identify you as a TPP.

Whenever this remains the same, no issues should occur. If your organizationIdentifier will change, then you need to recreate all active consents.