Pollen.

This is produced by plants seasonally of-course, usually once a year for a short period, sometimes only during the heat of the day when a specific temperature is hit.

The effects of this particular pollen are profound, hallucinations, visions and reckless behaviour in the vast percentage of the population. The effect is indiscreet sexual relationships, risk taking behaviour and lack of focus on things necessary for survival. This generally de-stabilises society and makes life difficult for everyone, people become desperate.

In a small percentage of the population, the force-sensitive ones (hell, who knows, maybe the pollen infected them with the midichlorians) it gives them all the same visions (or parts of the same visions of their future). When these people start to realise their common visions, they start to put the picture together - a vision of Corruscant - and the way to get there. These gifted individuals band together and lead the way for the whole population to travel to the new galaxy.

Their return leads to the same symptoms for much of the population, but the force-gifted ones, where will the force lead them, what is the force's will now 50,000 years later?

Very alien aliens

The planet looked unoccupied during the first scouting missions, but there was a previous owner and he attacked them after while or send an ultimatum. Maybe its an AI or hivemind which has merged itself with the biosphere. Or some ancient sleepers like the Necrons or Cthulhu, whose vault were hard to spot in the beginning.

Maybe those ancients even gave them the technology and told them never to come back. Now your protagonist has come back.

Economics

There is no valuable resources on Nu Terra, but plenty on Coruscant.

Once the crystals were discovered and enabled the humans to travel to and from Coruscant, the first to go there and return returned with unimaginable riches in gemstones, minerals, precious metals or other things that are highly valuable (or useful). The local environment is perfect for settlement, maybe the plants on Coruscant is directly edible/bears edible fruits, the animals are docile and delicious, and the land is exceptionally arable

At the same time, except for being marginally habitatable, Nu Terra does not offer even the most basic resources to build any permanent settlements or anything that could sustain them, maybe the plants their is not edible, and agriculture may be difficult due to the local conditions, or just because there wasn't any metal ores to replace whatever (very limited) tools the human colonists have brought with them.

Therefore, because there is a huge drive to develop industry and obtain resources, and for general quality of life, the humans quickly abandoned Nu Terra to settle Coruscant, they may even be forced to look for resources there because the supplies they brought there won't last more than a month.

Small settlements will last a while, as you can bring resources from Coruscant back to Nu Terra, just not very efficient. It's just better to do the mining and processing/manufacturing on the same planet, which means that there is no back and forth movement.

As a lack of usable resources does not go away with time, it certainly will last for time far longer than 50000 years, and still be present when the characters return.

Disease

It's been wiping out lifeforms for millions of years. It can be frozen in glaciers and permafrost. It could wipe out humanity and then die out leaving no trace except for more frozen sources preserving it.

Currently humanity is finding new viruses still viable in the melting permafrost due to global warming.

A disease that is fast spreading and 100% fatal with no known cure would cause the unaffected to flee the planet.

See Arctic Meltdown

Relics of an ancient civilization. Think of the Reapers & Protheans from the Mass Effect universe.

They land, all seems well. Ruins are eventually found, once activated it displays a message of inpending doom. The galaxy cleaning squad is coming to town really soon. Leaders keep it under wraps, scientist panic and go public. Civilization panics. One techy finds the crystal, another finds out where the previous owners of the planet fled to: Coruscant.

Could it just be that Nu Terra is an awful place to live, but at least it's better than Earth?

i.e. Earth has been taken over by the Plague, has an imminent gamma-ray-burst / solar flare, is about to be demolished to make way for an interstellar motorway, or for whatever reason they've left for the only other known planet that could possibly support life, Nu Terra.

But conditions are very difficult there and while they can technically survive, survival isn't very nice - temperatures are too low, there isn't enough water for everyone, the air is difficult to breathe, food is hard to grow. Then they discover this crystal which allows transport to the relative paradise of Coruscant.

If it is Star Wars universe, than the answer is obvious. The Force. The Dark Side of It.

Nu Terra has a huge lot of those "force crystals" and is evercorrupted with Dark and slowly corrupts everyone who lives there. It can even have evil "force specter"'s civilisation hidden on it! A huge plot engine!

It was an unexpected move.

Someone stored the crystals abit too close to the main power lines on their ship. When they turned their ship on up for a sub-orbital hop around the planet the crystal was powered up and activated. It then sent then ship though hyperspace to their destination.

It was always your second choice

Your scientists already had scans of Coruscant (somehow). These scans show it as developing as a paradise world - in fact, due to light-lag, it probably already is. By comparison, Nu Terra is awful. Humanity can just about eke out a living, but it's hard going.

On the other hand, the time and effort required to reach Coruscant was deemed far too much. Nu Terra is within range, we can all get there without too much difficulty. And we need to bail fast, before the oceans boil and we all die.

But, once you get to Nu Terra, someone starts experimenting with these weird new crystals. They figure out how to grow them, they work out how to use them for FTL scanning and communications (and, wow, Coruscant looks even better than we expected), and then someone manages to create an FTL Hyperdrive with them.

Suddenly, Coruscant isn't generations away. In fact, recharge the Cryopods we used to get to Nu Terra, and we can be the first to set foot on Paradise. We landed barely a month ago - most of the cargo hasn't been unloaded yet. And it certainly beats scrounging the mud-plains for bogworms to eat again.

When, whenever how long later, your characters return, the planted crops and the animals that weren't rounded back up have spread, making the planet... slightly more hospitable.