I don't know if this is help full but it appears the Governor Flanagin did help return the state archives to Federal Control.

Flanagin did participate in the last governors’ conference held in 1865 following the news of General Robert E. Lee’s surrender. At that point, the governors decided to seek terms from the Federal government. Opposed to continuing the war or conducting guerrilla operations, Flanagin returned from Texas and suggested to Federal authorities that he be allowed to summon the old legislature, repeal all acts of secession, and then resign. Under Federal military auspices, Arkansas Unionists had written a new constitution in 1864 and installed a loyal governor, Isaac Murphy. Thus, the military never considered Flanagin’s proposal, which would have implied the legality of his regime. He was allowed to return the state archives and retire unmolested to Arkadelphia.

http://www.encyclopediaofarkansas.net/encyclopedia/entry-detail.aspx?entryID=104