Farmer D
In the Brooder
I'm a certified organic farmer too, with a mobile flock of 28 field-working layers. I wouldn't hesitate to confine the birds for 5 days (after ventilation issue is solved) to allow for safe management (i.e. getting them in the coop at night). It's a one time thing, and for their own health and safety, so you can do it without jeopardizing your certification status. Unless you had a certifier and/or inspector tell you specifically you could not, I would do it!