@anon73 I managed to salvage your save.
My theory to how it happened is that during the process of dumping, one less byte was written,
so as a result your save appears corrupted (and too small) to PKHeX.
In order to save your save, I placed a "zero" at where it most likely got shifted,
and that place is your box 2 slot 13.
So whatever Pokemon was there, it's now gone.
However, at least you got your entire save back. main(2)1
Remember to rename to "main" when injecting.
Also back up multiple saves, before doing any injection.
Your SD may be dying, you might want to get a new one.