When you’re running a longer campaign, there’s always a danger that the story arcs you had in mind at the outset won’t be the best option as you progress through the arc of the campaign itself.
This is often a good thing: Static, predetermined stories can be awesome, but they can also feel static and predetermined to your players — not so good.
Planning things out in broad strokes (or even in fairly specific strokes) early on is a great approach. It keeps you focused and on-task, and it helps to ensure that your campaign feels coherent and shows progression over time.
But if you don’t think about the plans after you’ve made them, they may become progressively less workable and enjoyable as the campaign marches on.

So what’s the solution?
Think of prairie dogs popping up out of their holes from time to time to check for danger and get the lay of the land: that’s what you need to do.
Step back from your campaign, try to pretend you’re not as close to it as you no doubt are after several weeks/months/years running it, and ask yourself one simple question:
Does this stuff still make sense and sound like fun?
Use whatever trick you need to in order to give yourself a fresh perspective on your plans, story arcs, campaign arc, and the game to date. Show your notes to a fellow GM, post in a forum, go someplace where you don’t normally do your reading and read things over again — whatever works for you.
Then, just consider all of the major upcoming elements of your campaign — even the ones that are already in motion — and give each one a couple of minutes of your time.
Will it work given where the game is now? How about based on what your players are most interested in at the moment? Does it sound like as much fun as it did when you first planned it out?
Take notes about your conclusions, and then apply them to your campaign going forward. That might mean keeping everything exactly as you planned, or it could mean ditching some things (carefully, and without disrupting your campaign) in favor of new story arcs and elements that better match where the campaign has actually gone.
That’s all there is to it — it doesn’t have to be a huge process, and it’s usually fun. Just remember: Be the prairie dog.
And if it helps you to make prairie dog noises while you do it, well, no one else has to know about that, do they?
Fun read and good advice, now if I could only get another long running campaign started . . .
I ended up utilizing this advice during my last long-running campaign. It started in 2e D&D and ended in 3.5, and when I planned it out, it was going to go in a VERY different direction than it ended. My players glommed onto (what I intended to be) a minor villain’s schemes and set themselves to stopping him. When I saw how interested they were in this NPC, I hastily rewrote my campaign arc to make this guy a more prominent baddie.
In the end, the game ended up being far less epically heroic than my original plans indicated, but I think it ended up being far more fun and interesting for my players, and that’s what really counts.
This is why I like to have several threads of the same story in a campaign. If players don’t care for one of two of the possible paths, usually they’ll take the third or fourth. Somewhere along the line, those paths will cross again, letting my players wander off on what they think is an unexpected tangent. In the end, all roads lead to the same place, they just take you different places along the way.
You make some very good points here. Like evil mentioned above, keeping several options open to the players in the form of story threads gives them the freedom of choice to get to where you want them to storywise without cramping them at the same time.