Missing stacks!

This happens periodically, for no apparent reason. Most, but not all, of my photo stacks have suddenly disappeared. It usually happens after I leave the photos alone for a month or so, before returning to editing.

The edit process I use results in an edited tif file and the original jpg file. I stack these two together, keeping things nice and neat.

This morning I went into my photos from a trip we made last year and 90% of the stacks are missing!

How can I prevent this from happening again?