To clarify this a bit: The problem is that you want to retire a 1024-bit CA root, and replace it with a 4096-bit CA root. To do this effectively, new clients

To clarify this a bit: The problem is that you want to retire a 1024-bit CA root, and replace it with a 4096-bit CA root. To do this effectively, new clients need to stop trusting the old 1024-bit CA root, or there's no point doing the transition. However, you still want certificates that you issue to be verified by old clients that don't know about the 4096-bit CA root. To solve this, you issue certificates with two alternate chains of trust - one up to the old 1024-bit root, and one up to the new 4096-bit root - and teach the new clients to check all the alternate chains. It's this last bit that required the code change in OpenSSL, which contained the logic error that resulted in this vulnerability.