When replacing the server certificate and key with a cert signed by a different CA than the one configured with ssl-ca there is no error or warning returned to the client that has executed the FLUSH SSL statement to re-read the certificate files, and no warning in the server error log either.

So it looks as everything were OK, but the next client trying to connect via SSL will be greeted with

ERROR 2026 (HY000): SSL connection error: authority and subject key identifier mismatch

IMHO the user executing the FLUSH SSL should receive an error, or at least a warning, about the ca-cert / server-cert mismatch.