Q: Photos effectively empty after repair

Similar issues of thumb images missing after Repair or El Capitan -> Sierra conversion are sdiscue]ssed in a different thread.

Edited photos in Photos App is missing after MacOS Sierra update

One solution reported for edited photos was to revert to the original photo. 

Another solution, if you use iCloud Library, is to re-sync with iCloud.  It seems the sync which automatically follows Repair does not restore missing thumbs.  However, if you turn off iCloud for the library on your mac, then turn it back on, the sync that follows will restore missing thumbs.  The example where this was reported used El Capitan Photos.  It might also work in Sierra. 

Do you use iCloud Photos?

What happens if you revert to original on one of these problem photos?

Have you done any disk cleanup or run and clean up software like CleanMyMac?

LN

My issue is a little different as I don't even see thumbnails with exclamation marks - just nothing. Totally empty folders &  albums.

That sounds like what I was seeing.  But not quite totally empty.  While there were no empty rectangles with exclamation marks, there were empty spaces where the photo images should be.  I found that if I double-clicked the empty space, a large empty space replaced the grid of empty spaces, as though the image had opened for viewing.  At the upper right of the blank image, was an Edit button.  Clicking the Edit button opened the image for editing, and the actual image appeared, sometimes after a couple of clicks on the Edit button.   At this point, reverting an edited photo, or editing and saving the edit changes for an unedited photo, led to display of the missing thumb image.  This is discussed in more detail in the linked thread.

If you double-click an "empty" white space, does the blank "image" open in an edit window?  Can you manipulate it as described?  Does you missing thumb image appear?