The answer to this question can be found in Chapters 16 and 17 of Because of Winn-Dixie. The basic answer is that Littmus W. Block came back to find that his whole family was dead and his house was gone.
In Chapter 16, Miss Franny Block, who is Littmus’s great-granddaughter, is telling Opal and Amanda the story of Littmus and his lozenges. She tells them that he was just a young boy when the war started. Even so, Littmus lied about his age and enlisted. He went off and fought in the war and when the war was over he walked back to Georgia. Miss Franny then says
And when he got home, there was no home there.
Opal asked where the home was and Miss Franny shouts
the Yankees burned it! Yes ma’am. Burned it to the ground.
We then find out that all of Littmus’s family died as well. His sisters died of typhoid fever. We are not told why his mother died. His father died in battle in the war.
The point of this story is that the sadness that Littmus felt was what inspired him to invent his lozenges. This is meant as a lesson to Opal and Amanda in how to deal with sorrow.