This example demonstrates how to add and remove nodes and links from a force-directed layout. The graph initially appears with three disconnected nodes A, B and C. After one second, the three are connected in a loop. At two seconds, node C is removed, along with the links A-C and B-C. At three seconds, node C is reintroduced, restoring the original links A-C and B-C. Every subsequent second alternates between these two steps.
This example uses the general update pattern for data joins. See also modifying a force layout with transitions.
This appears to do the trick in V4 though I've not played around with the code yet.
https://bl.ocks.org/tezzutezzu/cd04b3f1efee4186ff42aae66c87d1a7