I just set up the WON version, and for some reason the HEV suit is gone when I get there. Also some npc's don't spawn in the same spots. I'm kind of at a loss here, any ideas?

you want to delete the saves inside "Half-Life\valve\SAVE", then instead of running "Half-Life.bat" you run "Half-Life (WON).bat"

^ this worked, thank you!