I am very new. to GIS. I am making an interactive that uses TopoJSON. Starting with a shapefile map of the world that shows the last bit of the Russia on the left rather than attached to the main Russian shape. I deleted the little shape on the left and modified the russia map to add the shape on the right. Export to mapshaper looks good. export to topojson and review on mapshaper, still god. bring into my interactive (using d3, yes this might be a d3 questions but I have to start somewhere) and the mystery shape is back on the left!
That piece of Russia is supposed to be there - the edge of your map in D3 (and many other GIS packages) is 180 degrees West. That edge cuts through Russia (hence why Sarah Palin could see it from her house), so D3 has cleverly chopped the Russian coastline along that edge and drawn it in for you in the right place.
The advantage of doing it this way is that if you use one of the D3 views that allows you to scroll the world around you won't see a spurious line through Russia where the two bits are joined. There is a reason all those example maps use a black fill.