You can upgrade it, but you need to pay the difference in miles from Economy to Upper, ( and taxes and fees) and you will get the PE voucher back into your account,
That said whilst that’s what should happen on 2 occasions for me the agent got it wrong and did upgrade the PE (having used a voucher ) to upper for just the extra miles. I know others have been lucky as well.
On one of my occasions I had a phone call a few days later saying the agent made a mistake, but they honoured the booking. On the other occasion nothing happened, I did sweat a bit when I checked in, in case there was a problem but nothing happened. I flew both legs no issues.
There’s nothing to stop you ringing and just saying you want to upgrade, and see what happens, you may get an agent who doesn’t know the proper procedure. And if they do know the proper procedure you can just say no.