-There's a really bizarre Spaghetti Western set in New Mexico involving gold, Gatling guns, and the inevitable appearance of General Sibley (he always seems to show up in Civil-War-era movies set in the West... I guess just to remind people there's a war going on!). The movie starts out with most of the main characters as Confederate soldiers, but they desert and hijack some gold-related business dealings between the North and the South. It's more of a setting than a focus of the plot, but still takes place in the time. It's called "Red Blood, Yellow Gold" in English, and, in Italian, it's called "Professionisti per un massacro."
-I haven't seen the movie, but "In the Electric Mist" is a crime thriller about a detective who keeps having flashbacks to John Bell Hood and his men while he investigates killings in his Louisiana parish... while a Civil War movie is being filmed in the area!
-Again, haven't seen this one, but "War Flowers" seems to be the old soldier-falls-in-love-with-nurse-type routine, based on the reviews on Amazon Prime.
-Do we count "Little Women" in any of its many iterations?
-Also, wasn't the protagonist of the tv show "The Virginian" a former Confederate solider?
-"Mercy Street" is a PBS tv drama that takes place in a Virginian hospital during the outset of the war.
-And, as an upcoming movie, "Antebellum" seems to fit in nicely!