Any time you make an edit on a clip with Neat Video or Warp Stabilizer applied, it will likely need to be rendered again to play smoothly.
The way around this is to add those effects after all of the other edits are done.
If you have your sequence setting preview codec/settings up to say a Cineform or DNxHD/R of the same frame-size as your clips/sequence, you can use Render/Replace on the full sequence, or Render Selection, Render In to Out or Render Effects and then the preview files become the basis for the work you're now doing. So you should be able to add color or other things without needing a re-analyzation from WS.
I just tried both ways ... a whole sequence (of a long clip) and part of the clip, segmented with Ctrl-K cuts to begin/end the section I added WS to. Render/Replace for the sequence creates a new media replacing the old, so the effects don't even show in the ECP anymore.
Render/In-out also allowed me to apply WS to the section, and then after it rendered, go ahead and do some other things without needing to re-do WS. And after closing/reopening the sequence, well ... it was 'baked' to the new look, with out the previous things selected.
So ... render/replace and render bits tend to be one-way streets. You don't need to re-analyze BUT ... whatever you've done is done. Unless you go back to the original clip.
I tend to batch effect clips in After Effects that I know are going to need treatment in Premiere Pro, including 1 light color grade, warp stabilizer, etc. Apply the effects, then run them through AME with the codec I plan to use as my previews and render codec for output. That way I can maintain a smart rendering workflow all the way through.
I only wish I could bypass AE add these effects right in AME as part of the ingest process.
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My workflow is to keep a second timeline open with the same settings as my master. If a clip requires an intensive effect such as Neat, I'll copy the clip to my secondary timeline, add the effect and add some head and tail trim, then export the clip from the secondary timeline with Match Sequence Settings and Import into Project checked.
This will "bake in" the effect in clip so when it is use that "processed" version I can add additional effects without burdening my system,
I believe this is a fine workflow that I might use. I was hoping to have the ability to make changes to the original footage if I should change my mind. (maybe to the NEAT settings a bit different).