I have no idea what will happen after another E4 run. It could fix the Hall of Fame. Maybe keep a backup and try it.
I noticed that the block ID of block A and B were wrong and block A contained data that doesn't belong there. Normally block A would store your Pokemon from box 5 but that wasn't Pokemon data. It looked like partial HoF data, but moving it to the proper offset wouldn't restore HoF though.
So I just removed the faulty data and restored the block ID and the save loaded again.