That is an interesting situation. About 5 years ago you did not need a day hike permit to day hike the North Fork and only needed an overnight permit to stay overnight. At that time, main trail permits were strictly for the entry via the main trail. Then the regulations changed to require all day hikers within the Whitney Zone to have a Whitney Zone day hike permit. That essentially put the North Fork and the main trail under the same quota for day hikes. Nonetheless, the regulations were not changed for overnight hikes. A main trail day hike permit will cover a North Fork day hike, but a main trail overnight permit only covers a main trail entry. Technically you could enter via the main trail and exit via North Fork on a main trail overnight permit, but a North Fork entry requires a North Fork permit.
Sorry for all the technical data. The current regulations were implemented at different points in time so there are a lot of gray areas. You may be able to cancel your main trail reservation and pick up a North Fork walk-in permit when you arrive at the Visitor Center. Just ask.
