EDIT:
WAIT...
I'm not sure but when transferring from DPP to HGSS do they go through the Pal Park?
If so then the following method won't make them Pal Park'ed...
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I like using this method for mass editing of pokemon
With a flashcard and DS Lite/fat you can use this save game manager to back up your save file from your retail game cart
http://projectpokemon.org/forums/showthread.php?12405-A-tool-to-backup-HG-SS-saves
then load your save file in to Pokegen, save each pokemon a .pkm file...
load your SoulSilver file, then load each .pkm and set them in a box slot
save that and then restore your file