If you open your save file in a hex editor (like HxD) you can visualize the 0x1000-sized save blocks for your data.
As you can see, the second slot has all block IDs present, while your other one has D,1,0,4 with duplicates containing different checksums. The games store box data in block chunks [3,D], and player data (progress, etc) in blocks [0,2]. Unfortunately, your backup there does not contain a block for #2.
I would try "transplanting" blocks (chunks of 0x1000 bytes) from the corrupt save into a donor save, to see what information you can recover. Maybe just overwriting the second save to see what data pops out in PKHeX.