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This does not seem to be an issue with the IncrementalUpdateStrategy, as following the same steps in the Sprotty viewer using the same strategy does not have this problem. The KGraph coming out of the incremental update also does not seem to show any difference between the first and the other nodes, so I would guess the issue is somewhere later in the toolchain, maybe when updating the KNodeNode representation or somewhere in Piccolo2D itself. As I don't know how any of that code really works, I don't think I can help you here right now without having a deep dive into the piccolo rendering.
Given the following graph:
If one changes the left padding to 10.0 and then back to 0. The node n1 is still placed at padding 10.
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