how does jonathan change as he experiences the conflicts in his life?

I think that Jonathan's belief in God grows. Jonathan repeatedly refers to positive outcomes - like the survival of his home and family - as “blessings” or “miracles”. Likewise, he believes that "Nothing puzzles God" in bad situations, like with the Coal Corporation's closing or with the climactic robbery. By imbuing God with the power to understand, Jonathan frees himself from agonizing about the seemingly random experiences of the Civil War and its aftermath. He may not understand, but God does. This allows him to use his energy constructively in the present instead of wallowing in the seemingly inscrutable past.

I think he changes by hardening his heart against any and every difficulties in life. By insulating his heart with a genuine deep faith in God, he developed a confidence which gave him the strength to rebuild his familial life. He learnt that only by working hard they could stand in the adverse situations. So, together they developed some skills and started working hard.