What you are seeing matches a recently clarified behavior. The normal autorotation path is a Key Vault poll every four hours, so a 1–4 hour delay is expected. Although the renewal page says any Application Gateway change triggers a check, Microsoft's newer troubleshooting guidance says that reapplying the same versionless URI—or making an unrelated/empty gateway update—may not force an immediate fetch because keyVaultSecretId did not change.
A different thumbprint, issuer, or root CA is not itself a rotation blocker. The new Key Vault version must still contain a supported, exportable certificate: PFX or PEM with the private key, complete intermediate chain, correct content type, and valid Key Vault access for the gateway's managed identity.
For a deterministic refresh, temporarily change the SSL certificate reference to the latest versioned secret ID, then restore the versionless ID. In CLI terms, run az network application-gateway ssl-cert update first with the latest versioned secret URL, and again with https://<vault>.vault.azure.net/secrets/<certificate>. This changes the value that controls the fetch while preserving future autorotation.
If it still does not rotate, verify the PFX/private key and full chain, identity permissions, Key Vault firewall access, and the gateway provisioning state.
Official guidance:
https://learn.microsoft.com/en-us/azure/application-gateway/renew-certificates#certificates-on-azure-key-vault
https://learn.microsoft.com/en-us/troubleshoot/azure/application-gateway/troubleshoot-application-gateway-key-vault-certificate#resolution-e-application-gateway-serves-an-older-certificate-than-the-current-key-vault-version-autorotation-stalls