Well these are two different things.
The PNR is the identifier of your booking. The e-ticket is a frozen state of that booking, which can be used for travel.
So your booking can be different than your eticket(s). However any flights that are in confirmed state in your booking, are available to be ticketed. The ticketing process basically means that they take a snapshot of your current booking, and assign an e-ticket number to that snapshot. This is what you then use to travel. This eticket cannot be modified, and needs to be invalided if your booking changes again.
The booking can be changed/updated to whatever they like. In theory they can delete all flights and add totally different ones. There should be no reason to issue a new booking/PNR. Personally I have never seen that happen either - over numerous rebookings with many airlines.
So generally when you are waitlisted they would add a new flight leg to your booking, in I class, with status 'waitlisted'. Once that status changes to 'confirmed' the old flight in Economy class will be removed from the PNR. The last step is that the ticketing department checks if all requirements have been met (eg all taxes have been paid) and if so, issues the frozen e-ticket.