I posted this as a response in another thread, but it has gotten very little commentary, and I don't feel it is being addressed, so I'm going to post this as its own question. I appreciate any input, and would really like to hear from an Adobe team member.

I have 2 Mac Pro machines that have recently been updated to CS6(Production Premium). This occurs on both machines. And is not specific to any one item being changed. It occurs to any changes being made AFTER rendering into PPro.

If I link between PPro & AE comps/sequence, I can make changes in AE and it will update to PPro as long as it has not been rendered. However, if I render the sequence in PPro, and then go back to AE and make changes(and yes, I am saving it before returning to PPro), it does not unrender the PPro sequence, and will not update.  It remains rendered in the sequence as if nothing has changed. No matter what I do to the imported AE comp in PPro, it will not unrender. (short of adding an adjustment layer with an effect above it all in the sequence to force it to unrender - this is my workaround for the moment).

I've gone so far as to delete the linked comp out of PPro, and re-import the AE comp, and if I drop it on the same sequence it pops immediately back up as rendered.  My guess is it has something to do with the global cache.

This is not a legacy issue, as this project was created from scratch in CS6.

Here's the workflow

Create PPro Proj  -> import footage -> edit video -> save.

Create AE Project -> edit composition to desired effect/graphics etc... -> import or drag comp from AE to PPro -> Lay AE comp on video layer above base footage -> Go back to AE make any desired changes and Save -> return to PPro, and project is updated -> Render ALL in PPro ->  realize something needs to be adjusted in AE -> go to comp in AE, make adjustment & save -> return to PPro and find that it will not update/refresh/unrender.

I'm aware of how sequences are affected when they are not pre-rendered. However, I'm specifically talking about once the file is rendered there is an issue that did not exist before CS6. In CS5 & CS5.5 I could render in PPro, make changes in AE, and the rendered timeline would become unrendered, and show the updated information from AE without having to manually delete any render files. I've done it thousands of times, and until CS6 it was not an issue. Having to manually delete the rendered file from the sequence defeats the entire purpose of dynamic linking - You make a change in one program, and it updates to the other without manual input - That is the point of dynamic linking.

Is there a setting in the preferences that I can change to make this work again? How can this be addressed without manually deleting the rendered file each time?

TL;DR - PPro doesn't refresh changes from AE once it has been rendered in PPro without manually deleting the render.