Can you describe a little more what you are trying to do? Your error seems to indicated you are doing polygon geometry edits but maybe you've made changes to your underlying geometry as well which is invalidating or "orphaning" some of these polygon edits? please describe further.
Sorry, I solved problem and forgot to reply.
Little more about a problem: I worked with quite extensive assembly and had to mesh it for Nastran SOL101 . First I started with meshig 2D elements, and at the end 3D elements and then started a problem (so you are right). Sometimes I had to cut some plates and solid bodies to achieve consistency of the meshes. Then the new unstitched edges occured and when I tried to stitch them the window from the first post occured.
The solution was quite easy, to avoid such problems run feature: CAE Model Consistency.
I hope It will be helpfull