"seems as if the axes limits are not getting updated as per the set values"
Set the axes limits after plotting:
figure;
ra = 0.5;
r1 = [4.662840968803412 -0.597125750259697 -5.446916224720714]*10^03;
r2 = [0.662840968803412 -4.597125750259697 -5.446916224720714]*10^03;
[X1 Y1 Z1] = ellipsoid(r1(1),r1(2),r1(3),ra,ra,ra);
[X2 Y2 Z2] = ellipsoid(r2(1),r2(2),r2(3),ra,ra,ra);
surf(X1,Y1,Z1); hold on;
plot3(r2(1),r2(2),r2(3),'*m');
surf(X2,Y2,Z2);
xlim([-10000 10000]);
ylim([-10000 10000]);
zlim([-10000 10000]);
Note that the axes limits are correct, but you don't see the ellipsoids because they are so small (radius = 0.5; axes-limits = [-10000 10000]). If you were to increase their radius, you'd see them:
figure;
ra = 5000;
r1 = [4.662840968803412 -0.597125750259697 -5.446916224720714]*10^03;
r2 = [0.662840968803412 -4.597125750259697 -5.446916224720714]*10^03;
[X1 Y1 Z1] = ellipsoid(r1(1),r1(2),r1(3),ra,ra,ra);
[X2 Y2 Z2] = ellipsoid(r2(1),r2(2),r2(3),ra,ra,ra);
surf(X1,Y1,Z1); hold on;
plot3(r2(1),r2(2),r2(3),'*m');
surf(X2,Y2,Z2);
xlim([-10000 10000]);
ylim([-10000 10000]);
zlim([-10000 10000]);
