I've tried and tried to get the edits to save with my Soul Silver save and none of them actually change in-game even though the changes ARE reflected in the save. When I load the EXACT same save in PokeGen the edits do not appear, however if I make them again with PokeGen, they show up in game.
I started noticing when trying to inject Gen 4 WonderCards with PKHeX which doesn't trigger the delivery man no matter how many times I tried (I triple checked to make sure I hit "save" in the WonderCard screen and the cards were not listed as "received"). So again I tried to use PokeGen with success as well.
It seems that PKHeX reads the save just fine but doesn't write for the most part. None of the edits I make take (pokemon, money, items, WC etc) even though they are reflected in the save itself when re-loaded in PKHeX. However, when the same save is loaded in PokeGen (after edits) they are not there, same as when it's injected.