If you have the PRT files, you can do several things:
*Scale the PRT Loader or even better, add an XForm modifier and scale its gizmo.
*Save the scaled PRT Loader back to a new PRT sequence.
*Load the new PRT sequence into PFlow using the Krakatoa File Birth / Update / ID Test (keep in mind you need the ID channel in your PRT files for this to work ok).
*Render your PFlow with Afterburn
or
*Load the original PRT sequence into PFlow using the Krakatoa operators
*Check the “Link To Object TM” checkbox in the Krakatoa File Birth and File Update - this will apply the transformations of the PF_Source object to your particles, so you can scale, rotate and translate your particles by just moving the PF_Source
*Render your PFlow with Afterburn
For more info on reloading PRT sequences in PFlow, see
http://www.franticfilms.com/software/support/krakatoa/using_krakatoa_particle_flow_file_operators.php
and
http://www.franticfilms.com/software/support/krakatoa/blending_particle_file_sequences_using_krakatoa_particle_flow_operators.php