A trade route does not "dissappear" over time. Once established, it will remain throughout the game, and I begin establishing some trade routes in BC or early AD. However, it can be (and often is) replaced by a newer trade route (at the instant a new, higher value route is established).
If the destination city is destroyed, the route will dissappear. One day, i decided to play an OCC conquer-the-world strategy, and I decided to require that I could never capture a city... only destroy it. As the enemy cities died, I had happiness problems in my city because the trade routes dissappeared as I destroyed the destination cities. A switch to Communism helped somewhat.
Also, a food route will replace a trade route (Civ 2 only retains 3 routes). Same happiness caveat.
But in summary, the change of commodities do not remove the route, at least in Civ 2 MGE... I use hundreds of routes in a game, and watch them...
On a different subject, the Civ 2 MGE AI likes to attack freight and caravans. I use this fact to start a war under Republic or Democracy sometimes... they are just too juicy a target for some of the hostile AI's to pass up... and they sneak attack, and bingo... war with no revolution. But the downside is you can't control the exact timing of the AI's sneak attack...
Like Shadowdale, I began playing Civ 2 and had never used Freight and Caravans, and thought they were too worthless to mess with. At one time, I had no idea how powerful trade was. But suffice it to say that when you deliver 3 to 10 freight each turn, and net up to 3,500 gold and 3,500 science for the trouble for EACH freight (late game, demanded cargo Uranium/Oil with airports)... it makes the lowly frieght the most powerful unit in the game, from a certain point of view. 50 shields = 7,000+ gold/beakers... not a bad return...