The link will break if the model it's position in the list (= index) is 'after' the node that references the model. To make sure the link stays intact, move the model to a position above the first node that uses it. You can use the green arrows to move chunks up and down. Most commonly, models are directly placed 'before' the first node that uses it, while materials are placed at the top of the file. After you've done this, you can fix the hierarchy again by temporarily specifing '0' as model id, and then specify the actual model id again. From here on, you shouldn't see the model jumping out of the tree anymore.
Note: It's easier to see the ordering in the 'list' view (the white-ish button in the toolbar switches between 'tree' and 'list').
It's a common error and I hope to add some form of validation at some point which ensures that S3D refuses assigments of models and materials that are incorrectly ordered, so these mistakes can't be made anymore.
PS: welcome to subsim
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