I have genealogical information compiled awhile ago (prior to the advent of personal computers) by my paternal aunt, the granddaughter of Augustus M. T. Flandreau. She received most of it from Betty Jackson, whom you mentioned in one of your posts. I would be happy to share those details if it would help. My aunt is no longer living, so I can't confirm my assumption that Ms Jackson has family records from which was compiled the Elder Daniel Alpheus lineage/descendant list.
Re: Daniel Alpheus Jr. who served in The Civil War, I dug up the following website with newspaper clippings detailing specific battles.
He is listed as one of the wounded in a battle on May 19, 1864. If you cursor down to the Morning Express article on May 24 and look at the entry for Battery G, you'll see him listed. (the May 23rd article from the same paper misspelled his name as Flanchan.) He served in the 7th New York Heavy Artillery. My aunt's notes have his death as occurring in 1869, so I wonder if he might have died of complications from having been wounded.