I lost all my stacks for some reason

My process for photo editing is to go into lightroom, select a photo for editing with Photoshop (selecting "edit a copy with lightroom adjustments) and then do a ctl-J in Photoshop to protect the original. When I save, I then have an edited tiff file and the original jpg (marked numerically 1 and 2). I then select these two photos and stack them. 

Suddenly, all my stacks are gone. I don't know why, but now I can no longer stack the same two photos without manually selecting them and grouping into a stack.
This ahppened to me a couple years ago too. 
Does anyone know why this happened so I ca avoid it in the future? Or an easier method of restacking these edited photos?

Thanks!