Orders remain in effect in Michigan, North Carolina and South Carolina, but each state is honoring a different person.
A weeklong directive will keep flags lowered through Saturday.
Gov. Ron DeSantis ordered Florida flags to also be flown at half-staff until July 18 to honor late Sen. Lindsey Graham.
The event faced programming challenges weeks before it began Thursday and has since experienced a bumpy start to its 16-day run.
An image of a Confederate flag was removed from North Carolina booth at the Great American State Fair, Gov. Josh Stein's office confirmed.