janjust
sounds like your "keys" directory is screwed up, and your .../keys/ca.key and .../keys/ca.crt files no longer match; if you don't have a backup you have no alternative and you will need to regenerate the CA (and all certs underneath it).
Check the dates on the ca.key and ca.crt files; when was the last change?
Also, the ca.crt file is public and is probably found on many boxes - if you've lost this file (i.e. the ca.crt file that corresponds to the current ca.key file) then you can simply replace it.
