I noticed after claiming the mandate as a Kingdom in my current game, that you still retain a (somewhat) hidden legitimacy stat. This is used for potential PU's and voting criteria for the HRE.
You can view it via PU's in the vassal interaction screen, as the legitimacy of a junior partner is that of the senior and increase it with the Papal +1 legitimacy option. (if you are catholic that is)
Not sure if there would be a hidden republican tradition stat as well.
Edit:
More on topic: Yes you will keep your ruler.