custom permalinks suddenly not working

I have a wordpress multisite installed, with many sites running off of it.

This morning I found that my main site that all of the custom premalinks no longer work and send to a 404 page.

They were all working last night.

They work on all other site on this multisite.

Nothing changed from last night. I reset the permalinks via the admin area, still dont work.

But if I use any of the premade permalink structures it works fine.

Any thoughts on this?