If you want to do further processing to any Warp Stabilized shot the best option is to apply Warp Stabilizer and then render that video to a suitable DI (digital intermediate) using a lossless or visually lossless format for further processing. You would have to do that anyway to use Mocha because Mocha uses the original video and ignores all effects applied to the footage.
Warp Stabilizing is a resource hogging slow to re-render mess of a system to try to use as a source for further effects work. I would never intentionally apply any effects to a clip in Premiere Pro if I were planning to bring that shot into AE because some effects do not come over well and effects that require rendering like Warp Stabilizer would have to render again.
I just ran a test on a short clip in Premiere Pro and the re-rendered warp stabilized shot in AE looked exactly the same as the warp stabilized shot in Premiere Pro. I'm not sure why yours is not working. Are you up to date with both AE and Premiere Pro?
Depending on the shot you may be better off working with the original, doing your tracking in Mocha, completing your composite and then either render the composite for warp stabilizing or nesting the composite comp in a new comp and warp stabilize the nested comp. Here again, if the shot was longer than a couple of seconds I would render a suitable DI for use in Premiere Pro.
Thanks Rick for the thorough information . I had rendered to a DI in the past, but was hoping to avoid that process. The source media is 5k Red video. It's still a mystery why the stabilization doesn't seem to be applied in AE. I'm sure a render would be fine (like your test), but why can't I preview it in AE?
If AE can't accurately import effects from Premiere, why does Adobe say that it can? Better to just tell people that the two apps can't share that info. I hate buggy mostly working features! And the interfaces between AE and Premiere are still miles apart.
Doing a motion tracking on a on already stabilized shot will make the motion tracking process easier, so I'll go the intermediate route. The only issue I may have is that I'm on a PC using ProRes as an intermediate (Mirazon version since Apple doesn't license it), and I've been having issues previewing and rendering it in Premiere because of the mess that is Quicktime. I've used Cineform in the past, but Premiere has had some pretty nasty bugs with it in the past, so I was forced to switch to ProRes.
I don't have any 5K footage to test but my 4K footage stabilize fine in the latest version of AE. I would be interesting to see maybe 100 frames of 5K footage to see how it behaves. If you have some or know of a source let me know and I will give it a test.
I truly appreciate the kind offer, but I spend too much time trying to debug Adobe software for them. I need to move ahead with editing the clip. Thanks though. You've been very helpful. Or are you interested in just having some 5k footage to play around with? I can try to post something for you later.