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Thanks for the example to reproduce! You're right about the problem. Perhaps we need to check for this happening and change to a different layout method if there isn't enough space to draw the link.
(The link outline is calculated by d3-sankey-diagram directly and filled -- it's not the SVG stroke-width that's causing the problem)
Take this data:
put into https://ricklupton.github.io/d3-sankey-diagram/
Observe strange layout if links from "a" to "c" (largest one)
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