I usually export the stabilised clip using a lossless codec, such as UT, then import the stabilised intermediate file.
As you have guessed this arises because the stabilisation is applied only to that part of the clip on the timeline, and when you add the transition, you are using handles, which have not been stabilised, so there is no "zoom-in".
I'm not adding a transition, I'm simply putting the clips beside each other (wrapped/unwrapped) .
The "warp motion" would still appear if you export though (and put it in the timeline)? No? I don't see what difference it would make.
Very tempting to drop the wrap over the whole clip (2min)..
But you said "transition" - first word, second line?
If you stabilise and export a clip with handles, you can then apply transitions without problem, to the new clip.
Applying the stabiliser to the entire 2 minute clip, if that is what you mean, would not work. There would be too much motion overall for the stabiliser to achieve an acceptable result.
The best results are always achieved with short sections of clip, so the total motion over the timescale of the clip is limited.
The jump happens on the transition between two clips (leaving one, entering another), it's a transition but I should've used another word perhaps.
Ah, I think I get what you are doing - the two clips on your timeline are separate sections of a single shot?
Yes, there will inevitably be a jump - just as if they were two separate shots.
Single shot yes.
What can be done to create a smooth transition in between the clips?
You could try to see how much the stablilised clip is zoomed in, add this zoom to the incoming clip, you might have to move the position of the incoming clip as well. I've not tried it but it might work!
This has been posted on many occasions.
Forget linking, stabilize clip, export it and use the exported clip
The stabilization will be even better if you do it in AE