In my view, the big thing here isn't so much the time-skip as what it represents — a series of large, unexpected changes to the world the characters are in. Instead of returning to find the "timeline" advanced a few years, it could just as easily be a fantasy apocalypse, or the PCs getting flung into another plane of existence, or even a smaller-scale plot twist like a war breaking out.
Do you need foreshadowing?
Foreshadowing is a very convenient narrative technique. I don't think it's ever required, but it can make big transitions much smoother. This is because foreshadowing creates a feeling of natural progression. You don't have to "give away" the impending setting transformation, but creating a general feeling of impending change makes it easier to accept. Good foreshadowing creates opportunity for positive feelings, since now the event itself will feel like a promise fulfilled. Without it, you risk players reacting more like you've pulled the rug out from under their feet.
In your case, you can play up the alien and dreamlike nature of the Fae realm. Make the PCs feel disconnected from their own world. Have a Fae being tell them something cryptic about time and change. You don't need to lay a trail of factual breadcrumbs or explain the temporal mechanics of their journeys, but it pays to establish a mood.
Mind the side plots
Players will often have "side plots" that they care about, typically involving characters' personal goals or relationships with NPCs. Abrupt changes to the setting can cause the players to become anxious or annoyed when those side plots are invalidated.
In this case, in particular, nearly all of those side plots are going to get twisted up pretty hard. Friends, loved ones, and rivals will have changed a lot. Many people will have likely assumed the PCs are dead and gone, and moved on with their lives in surprising ways. Their resources and power bases, such as guilds and strongholds, may not be available to them anymore. Maybe the reputations they used to have are long-forgotten. Maybe they've been declared legally dead. Maybe their homeland is a smoking crater. Some of this is tough stuff, so much so that it's like a punch in the gut to hear it.
It's good to sit down for a moment and explicitly identify the most important "side plot" stuff before you introduce the big thing. That way you have a sense of how the PCs will actually experience the change in play. You can also identify "side plots" that you want to explore before you actually do the big change.
You can use the time-skip to put the characters' resources and relationships in jeopardy, but I would avoid outright destroying them all. When the setting has changed a lot in one fell swoop, the players will be looking to reliable and familiar connections as anchors to help them understand and care about the new world they're in; they still need reasons to fight on, after all.
Raise the stakes, but don't turn a victory into a failure
More often than not, the big new twist involves a setback for the PCs. That's part of raising the tension of the story. An event that makes the PCs' lives harder, brings suffering to supporting characters they care about, or empowers the villains will feel like a major defeat. What's worse, it can feel like an arbitrary defeat they couldn't avoid. Thus, you'll usually want to mitigate the setbacks with an important victory.
In your case, the heroes have gone to the Fae realm to gain something they can use against their enemy, right? If they return to find their enemy is more powerful than ever — well, that information better be worth it! Otherwise your time-skip is turning a modest victory into a terrible defeat — not a great way to use a concept that many people will be naturally a bit wary of from the get-go. So, make that secret knowledge from the Fae really, really count!
Big world-breaking events you can't control feel disempowering to players. That doesn't mean you shouldn't use them. But be mindful of the details so you're not making that disempowerment excessive or pervasive. Give them plenty to do in their new environment and make sure they have some touchstones to reconnect with the old one.