Hi,
We can book only one appointment at the VFS with our express entry application number. So when you have your new passport in hand, if you go to the VFS on the old appointment, they will not accept it.
Also, if you try to create a new booking, the system will give you an error saying you have already an existing booking on the application number.
So you need to cancel that and get a new appointment.
Write to
Passportsubmission@vfshelpline.com
And mention that you need a new appointment as you are going to resubmit your passport.
VFS folks will take one or two days and they will let you to create a new passport submission appointment on your express entry application number.
I hope I answered your question. Please let me know if you have anymore doubts.