As far as I can discover there is no library.museum collection of Henry O. Flipper papers. Some items, written long after he left the army, are held by members of his family.
As far as I have found, and believe me I have looked long and hard, there are very few surviving documents in Flipper's hand from the period of his military service (mid-l876 until his dismissal in June, l882). This is very frustrating because I suspect Flipper wrote and receive a fair amount of letters--and I suspect that he may have kept a journal. But if he did, this source material has not survived--or has not been found.