Hi Richard,
Please correct me if I'm mistaken.
The secondary verification certificate is suppose to be supplied by the federation partner. In case the federation partner (be it SP or IdP) do a cert renewal on their end, we can use the secondary cert that they supplied to verify their signature in saml request or response.
on the flip side, we can provide primary and secondary certs to the federation partner so that they can use both certs to try and verify our signature if and when we do a cert renewal at our end.
Having said that, this seems to be only meant for Signature verification.
The "secondary certificate" mechanism isn't available for encryption and decryption part of the assertion processing flow.
So if anyone implements assertion encryption, and needs to do a cert renewal. A collaborative effort is required between IdP and SP to apply the new cert at the same time and downtime is expected. So there is going to be operational impact in such cases.
regards,
Zen