Looks like what you are observing is in the backup save.
It's likely that PKHeX only edits the bytes in only one save location, not both (normally you game only loads the most recent save).
If you want to check for it, try loading the edited save in-game, save twice, then load the new save into a hex editor.
If you look at other pages of saves in the same era (such as this; see the second paragraph), you'll discover that there's actually 2 saves block per save. The game actually keeps 2 saves, just in case you corrupt one, you can load the other.