Certificate authority removed from forest

[localzuk]

We have a system here which used to be part of a managed service, and as part of that we have a 'forest' of domains (basically a top level domain and the one in the actual school).

When this was running as the managed service, the provider had a certificate authority in place, which obviously handled all the certificate demands of the network.

Now, however, they didn't leave it in place so we have a system that is referring to that CA which doesn't exist, and certificates are basically starting to expire and things are gradually going a bit odd in places. For example, Spiceworks can no longer connect to AD via SSL.

How do I go about adding a new CA of our own, and replacing all the references to it?

[localzuk]

Can I simply follow the instructions here to remove the CA(s)?

http://terrytlslau.tls1.cc/2011/04/decommission-windows-enterprise.html

There appears to be reference to half a dozen of them, all BSF ones.