Ah, the bane of airliner modeling. Not an uncommon experience. Not an ideal solution, what I do is try to build up the missing window with window cement, like MicroScale Kristal Kleer. If the window is not too big this will work, though it will look different than the other windows.
If that does not work, here is a harder method, but it may work. File down the edges of the window a bit with a needle file so it fits into the hole from outside. Then, put window cement around the edges of the hole in the fuselage. Now put a piece of masking tape over the window and trim it larger than the window, by at least 1/8 to as much as quarter of an inch around each edge. Slowly insert the window into the fuselage. The tape should hold it flush with the outside of the fuselage if you don't press too hard (press on the tape hanging over, not on the window area itself). Then let it set for a good 24 hours and remove the tape. You may need to clean up a little, but it shouldn't take too much. However, be careful- it will be a very weak bond.
BTW, maybe you should also ask in the airliner and civil aircraft forum, the next one down, since it is such a common problem on airliners.