i'll look into it... right about now.
hrm. the messages aren't switching properly, but i have a good idea why you cannot close those routes.
For the aircraft you have each departing on routes from LHR and LTN, so the route bridging the two cannot be closed (as the plane cannot magically jump the gap between the cities). the system should be saying "you cannot close this route because it joins other routes the plane is on", but instead it's saying it's successful. hrm. i shall look into this more thoroughly, but there's your answer....
ah. i see why. the exact thing i said cannot happen is happening (it's actually possible, but hard to achieve).
you broke it. i really need to upgrade the point where that breaks.
edit: allow me to explain better.
when two focus cities are close together, there's a chance an erroneous route closure can take place. with 9879 this route IS closable when it shouldn't be, and the other isn't close able because of this exact gap. when the game detects a probable split it says "nope, can't close this route", if you somehow successfully sever a plane's routes into two like this, it suddenly thinks no route is valid to close.
Now, the solutions to this can be annoying, either you can (i the case of 9879, which i had to reform by the way, sorry.) back your way out of one of the focus cities so the route you want closed is valid; you can eat the loss on that one route for the benefit of the remaining routes and just leave it intact, or (in the case of t'other), you can view ac info, click close all routes on plane. This means you'd have to redo all the routes on the plane, but it should free you from the gridlock which inadvertantly occured.