I've had a carbon steel pan with some thin flash rust spots. I've tried to remove them by scrubbing, but after applying a new layer of seasoning it turned out I hadn't removed all of it.
While I find a lot of posts online about how to remove rust from pans and how to prevent rust in pans, I can't find a clear answer to the question whether a thin layer of rust under layers of seasoning is actually harmful. The way I see it, once there's enough seasoning on top of the rust there won't be any oxygen for the rust to expand and the surface that touches your food is free of rust.
What are the downsides when you have some flash rust in a carbon steel pan and continue seasoning over it until the pan stops giving off rust when rubbed with an oily paper towel?
Some of the problems I can imagine happening (but I'm not sure if they will happen):
The seasoning won't hold onto the pan as well as it would without the flash rust.
The new layers of seasoning won't 'grab onto' the rusty parts meaning that you will never arrive at a point where the existing rust is trapped inside layers of seasoning. In other words, when rubbing it with an oily paper towel the pan will always continue giving off some rust.