Because you had no minisaves folder, all the chests are empty.

Because you have a minisaves folder now, all the areas stored in the minisaves folder were created with empty black chests and will stay empty until the areas respawn.

What you need to do now, is delete all the files in the minisaves folder one more time. That will force each area to respawn and the game will use your new hexeditted HDR file to fill the black chests with random stuff.