The only thing you need to do before the re-formatting of your system disk, if you haven't already done so, is to save a copy of the plugin installer file(s).

ProTools authorisations are carried on an iLok key.

Powercore versions of the plugins are authorised against the 'authentication ID', so travel with the PCI or Firewire hardware.

After you have initialised your disc and reinstalled your system software, you will need to re-install the plugin software, using the installation file, and it should all run correctly, when you start your next session with the plugin.