Timewarp problems in AE CC with clips linked from Premiere Pro CC

Hi guys.
I've been searching for answers for a while now and hopefully you will be able to help me with this issue.
I have a project in Premiere Pro CC and I am using a "Replace With After Effects Composition" option on a clip which is cut from a longer video.
Then, in AE I am trying to use a "Timewarp" effect which instead of working only on this short clip, works on the entire video thus what I see in AE is not what I cut in PP because clip is slower and "moves" on my timeline. Because it's a linked comp I am losing the bits that I want to work on.
I am aware that clip needs to be longer for "Timewarp" to work and I was also trying to PreCompose my video file but whatever I do the same thing seems to be happening.
I know that I could export this short clip and then import it in AE but I have many of them and I want to be able to come back to AE in the later stages of the project and apply some changes which I will see in PP straight away.
I hope all this makes sense.
I am attaching two screenshots.
Thanks a lot!

When working with time manipulation it's better to just take the clip into AE, do your magic, render the result to a suitable production codec and then drop the rendered clip in your PPro timeline.

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