The Caspian Sea disappears on this example with .rotate([107.1,-78.6,-162])
it disappears with all versions of d3v4 (from https://unpkg.com/d3@4.0.0 to https://unpkg.com/d3@4.11.0 ).
EDIT: the problem lay in the json file that this example uses. Fixed with latest https://unpkg.com/world-atlas@1/world/110m.json
Original research by Philippe Rivière for d3-geo issue #121.