Partial Savefile Fix Tool 1.0.1

What it can do, is replace invalid blocks with valid blocks from community saves, so that it can once again become usable with PKHeX.

To use, select the correct game save type (example: Pokemon XY) and click on the "Standard Fix" button. (ignore Box/Slot and Pokemon Box Salvage for now)
After the fix is done, load the file in PKHeX so that PKHeX can fix the checksums, then export it from PKHeX as per normal!

If you see chains of red blocks like these below, you may want to use Pokemon Box Salvage mode as well.

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.