I don't know if this is the same thing, but check the size of the file on the SDCard if you are slicing to the HDD than copying to an SDCard.
I have had an issue when doing this sometimes.
Simplify3D says it has finished slicing and so I immediately copy the file to the SDCard.
In my case, the little Intel NUC that I now slice on was still in the process of grinding through the slicing, and so I was copying an incomplete/empty file to the SDCard.
My fault, not Simplify3D.
I don't usually get caught by this as I am aware the little NUC struggles - just now and again when slicing really large complex objects and I'm not paying attention.
If it is the same issue, the file sizes will be different between the card and the HDD.
I hope this is the solution for you.