Since by design, you cannot recover from a CA root certificate expiring, sometimes you need to limp along, and continue to issue certs even though you cannot necessarily revoke them, because the CRL published in Active Directory is now incorrect, or offline.
While we can argue all day about the benefits/detractors of this, here it is:
To bring the CA Root back online after the Root certificate expires, issue these commands in an elevated powershell:

certutil –setreg ca\CRLFlags +CRLF_REVCHECK_IGNORE_OFFLINE
net stop certsvc && net start certsvc

Now, go back to the drawing board, and PLAN your PKI implementation, and DON’T LET YOUR CA ROOT CERTIFICATE EXPIRE!!!

Incidentally, once you’ve fixed your certificate snafu, to stop ignoring offline CRLs, do this in an elevated command prompt:

certutil –setreg ca\CRLFlags -CRLF_REVCHECK_IGNORE_OFFLINE
net stop certsvc && net start certsvc

Give up?
It’s time to upgrade your version of Windows!!
http://www.us-cert.gov/cas/techalerts/TA09-209A.html
If you don’t know what that means, you’re in trouble. Yes, you.
Basically what this says is that EVERY version of Internet Explorer on every version of Windows is vulnerable to a Remote Code Execution exploit. (in English, that means that Mr. Bad Guy can run *ANY* program he wants on your computer with full administrative privileges. This of course, being in direct violation of Rule #1 of the 10 Immutable Laws of Computer Security.)
The patches will implement a kill-bit, and disable parts of COM and ActiveX controls, p(robably)ossibly breaking legacy applications.

The solution?
Run out ->don’t walk<- and buy the latest copy of the Microsoft Windows 7 Operating System. Oh. Sorry. You can't get it, just... yet... It's coming, though.. Microsoft Partners will see it in about 2 weeks, and it will be available to the general public some time in October. The attack vectors are not only via Internet Explorer. Any application (such as MS Office) with access to ActiveX and/or COM objects can exploit this vulnerability. Here’s the bulletin. Extensive testing is suggested if you use ActiveX controls or COM objects in mission-critical applications.