I'm not sure if this will help, but it's an excellent tutorial on the subject: Encrypt or Decrypt a Folder or File
. Reading it, you may note at the beginning there is a link to a 3rd party program (it's a trial version so use it to fix
the problem and then cancel the trial) for difficult situations and yours seems to fall into that category. You can check the rest to see if anything helps, but I suspect you'll end up coming back to needing this program. There's no guarantee it will work (although the list of what it can do is impressive, it doesn't specifically include encrypting the certificate - but it's certainly worth a try).
I hope this helps.