So this is a mystery to me. I made a dynamic link composition in AE to do some de-noising. I went back to the timeline in premiere CS6 and clicked a clip and choise to replace it with a clip form the bin which was the linked AE comp. When i do however none of the effects applied in AE are on the clip, even after rendering. Any clues?
Are you using Magic Bullet Denoiser? I don't have that particular plug-in so I can't test it, but this works fine for me with other effects. A possible workaround would be to render the clip from After Effects using a production codec and replace it manually.
If you're not seeing changes in an AE comp in Premiere then you didn't use Dynamic link properly. There is no possible way that a dynamically linked AE file cannot reflect changes in that comp in Premiere. It's just not possible.
Here's the basic workflow from PPro to AE and Back. Select a shot or shot's in PPro, right click or select from the menu Replace with After Effects Composition. AE opens, loads the footage and tells you to save the project. You make your edits. You can then leave AE open or close it. Back in Premiere your AE project and the specific comp you were working in is now in the timeline. If you need to make other changes in this comp all you have to do is open it and make the changes, then save the project. When you do the Premiere will read the changes. If it doesn't then you're looking at a cache issue. Close your PPro project or flush the cache and try again.