A little of both. Some are ''laid up good order'', or stored serviceable. Others are ''laid up bad order'' and will never run on BNSF again as they will be sold. Some like the SD9's are LUGO but will be sold because they are just plain old.
I hope that some of those rust buckets are not stored as serviceable. I recently climbed up on a SD-40 with a new swoosh paint job, tripped on the top stair and put my foot through the steel panel below the hand brake, pure rust! I've had more than one, in recent times, when making a hard joint, shake gobs of rust out from the bottom of steel panels. On many of these engines the only thing keeping them from falling apart has been the paint.