Will they heal? Will they stay ruined? How will saidin's cleansing affect them? Discuss.

I believe there will be no change to the ways if it was damage like that only from the taint when it was made, just like madness in the channelers it wont go away with the clensing, however i believe they can probably remove the taint from the ways somehow just like nynaeve can remove taint from peoples minds, (although  a very different process), I have no idea whether it could self heal itself afterwards or not.

i think the Ways disappeared because basically they were not mentioned at all in aMoL.  

The ways were mentioned. That was how the Trollocs got into Caemlyn. Also, I agree with Rand4747. 

I think RJ has been quoted somewhere as saying the Way's won't heal.  Something about removing the chemicals wouldn't remove the bacteria they had caused (i.e. cleaning saidin wouldn't remove the taint).

If Balefire can destroy mashadar, then maybe it can destory Machin Shin as well.
Then again, maybe the most destructive force in the world isn't the solution...

Likely, the Ways will continue to deteriorate until they become completely inaccessible.  After all, at some point, the Ways have to go away so that tainted male channelers can gift them to the Ogier who provide them sanctuary in the next Turn. 

Hordes of Trollocs seem to be going through the Ways in KoD and aMoL.  This seems inconsistent with the Black Wind hunting down the Trollocs; I think in the earlier books only 50 Trollocs could go through at one time.  I don't think we've had a major character use the Ways since tGH, though I could be wrong on this, as I haven't read the early books for a long, long time.

 

If the Ways were to heal, they would provide a way for ordinary people to get around quickly without asking a channeller to open a Gateway.

Machin Shin must be destroyed before the Wheel reaches the Age of Legends again. However, the waygates must also be destroyed at one point or another before then, so it is likely that channelers will destroy Machin Shin, and then (perhaps in another age), the Waygates themselves will be destroyed in some turmoil.

I wonder. Is that really necessary? The waygates essentially created an alternate world right? Why would the continued existence of the current waygates stop Aes Sedai from making a new set?

The ways were mentioned. That was how the Trollocs got into Caemlyn. Also, I agree with Rand4747. 

 

didnt the trollocs attack in ToM?  

 

I get confused after reading the prologue 6 months before the book...haha.

They access another world. The Aes Sedai simply bridged the gap between the two. That world must be cleansed, because it also has a place in the wheel. Even alternate worlds should theoretically return to their previous state. I may be wrong on this, but even though the Aes Sedai should simply be able to use another world next time (small change), the world that is contaminated should need to return to its original state (would be a very large change).