It did not appear to have hit the flaps - the outboard cover was still attached after takeoff and was entirely above the wing and the inboard cover spent its time on the loose over the wing as well. The outboard cover appears to have banged up the top of the nearby slat, but the dents on top aren't as bad as some I've seen from hail damage.
I'd go for excessive caution, but given the entirely unknown situation and being unable to observe beneath the wing, with the option of the long runway they had, it was a reasonable choice to take it.
Most likely the tires are heading for a retread and the brakes will need a look; both a small price vs the potential cost of damage to the horizontal stab if a cover let loose at a higher AoA typical during landing.