I haven't logged into our Apple push portal recently, but I believe we have at least 4 or 5 different push certs there, so there should be no issue with adding additional ones. So, no, choosing Create new certificate has no impact on the current ones.
One piece of advice though - If you're not already doing this, I would take advantage of the fact that Apple's portal allows you to add notes to the push certs. I have done that so as not to get confused about which one is which. A simple note showing which server it was generated for or what it's purpose is goes a long way toward preventing future confusion.
