As seen in the example above, Red Box starts from Box 2, Slot 13.
Now, Drag in the unedited and unfixed save file,
Select Save file type (example: Pokemon SM) and correct Box and Slot number (example: Box 2, Slot 13), and press the Pokemon Box Salvage button.
The new save shall look like the image below. (Note: the corrupted Pokemon, which is the first red slot, is lost forever)
As you can see, the other Pokemon have been salvaged! As usual, export the recovered save from PKHeX (to fix checksums)
In such cases, I won't recommend continuing play-through on such saves. Extract the Pokemon you can salvage from PKHeX.