You can use the XData and YData property of the graphPlot object to fix their position. Check the following example
G = digraph(1,2:5);
G = addedge(G,2,6:15);
G = addedge(G,15,16:20);
subplot(2,2,1);
Gh = plot(G);
x = Gh.XData;
y = Gh.YData;
rand_edge = randi([1 10]);
G_new = rmedge(G, rand_edge);
subplot(2,2,2);
Gh_new1 = plot(G_new); % changed position of the removed node
subplot(2,2,3);
Gh_new2 = plot(G_new, 'XData', x, 'YData', y); % edge removed but nodes at same position
