unthreading and retheading cs6

If you've scrambled the frame flow of a large document, it's likely you made a number of unwise moves (literally), and I'd have to wonder if the document was set up correctly (all best practices, as a single, clean flow, etc.) to begin with. Applying fixes suggested in good faith could make it all worse.

Honest answer? You can probably sort it out, with enough effort, patience and suggestions from here... but the straight line solution is to start over. Create a completely new document with the right basic page structure, and cut and paste the old doc into that new, single flow. Then reformat and clean up, one page at a time. And clean up any style issues as you go.

I know; that sounds overwhelming. But it will probably use less time, and generate a cleaner, un-broken result that will accept more editing and changes gracefully. Hacking together a fix on the broken one will likely leave many broken things, waiting to trip you up on subsequent work, editings, export to any format but print-PDF, etc.

The takeaway here is that shortcuts are almost never the right choice with ID documents. Everything is connected, not always obviously, and it's easy to do simple things that might seem speedier or more efficient but have dreadful consequences.

My US$0.02, from (too) much experience with these things.