Gondwana is one badass supercontinent. Present day estimates put its surface area at a bafflingly big 100 million km2. For comparison, Asia is about 44 million km2. This means that Gondwana has nearly about 2x as much area as the largest continent on current day Earth.
Now assuming that your aliens managed to collide India, Arabia(Tethys), Africa, Antarctica,
Australia Oceania and South America together (Remember that Gondwana wasn't just South America and Africa, it was a combination of many more tectonic plates), then you are in for a bash.
First of all, assuming that the Indian plate recedes away from the Eurasia plate before Gondwana 2.0, you are gonna get a pretty big chunk of the Himalayas being torn apart. Maybe Mt Everest or some mountains will not get smaller due to the sudden tectonic reversion, but it doesn't matter. You have a frigging mountain range being torn away from a giant tectonic plate. But for now ignore that.
Now, as the 6 plates collide, you are going to have a tectonic mashup at the Southern Hemisphere. The area where South America, Africa, Antarctica, India and Arabia (Tethys) collide, is going to suffer from immense tectonic stresses due to multiple plates banging against each other. This means that some of the plates will subduct, while some just compress against each other and produce fold mountains, like the Himalayas. The area where the subduction happens is going to have a metric f**kton of volcanoes, as water seeping in with the tectonic plates trigger rapid decompression events which melts mantle material into magma that rises up and builds up pressure inside the crust, and erupting out of the surface. This would happen in the central region, where the plates collide. However some plates may not subduct, and instead just compress against each other, producing fold mountains, like the Himalayas. Antarctica may still retain some ice, depending on how far north it moves forward to collide with the other 5 plates to form Gondwana. Australia/Oceania might get some underwater mountains/volcanoes, but Oz and NZ will pretty much remain the same.
However, let's move onto the biomes.
The coastal climates would be pretty much just be normal, except at the Indian coast, there would be a bunch of mountains standing there, which as you guessed, are the Himalayas which got torn apart. These Himalayas will prevent any oceanic winds from entering the Indian plate. India might face a huge rain deficit, but soon this may go away, as wind patterns readjust and enter mainland from another direction. Africa and South America are going to experience a b*ttload of rainfall. Remember those mountains (and volcanoes, most of which would have gone extinct in a hundred years)? This produces a barrier, which prevents oceanic winds from passing away from Gondwana. This means that the Sahara will be heavily inundated. The volcanic ash from the now-extinct volcanoes could have earlier settled over the Sahara, meaning that the sand is now impregnated with hundreds of nutrients. As the sand turns into soil by continual erosion, billions or even trillions of trees are going to grow on this land, turning the Sahara from a desert to a rainforest. Most of Gondwana would experience a tropical climate due it it being close to the equator. But Southern Gondwana is going to be subjected to a lot of snow, as it is extremely close to the south pole. And well, the mountain ranges themselves are going to be very cold as they are located at an extremely high altitude, which means you should expect a lot of snow in the central region.
Central Gondwana- Frigid and Snowy biome.
Southern Gondwana- Extremely frigid icy biome.
Coastal-Parts of Central Gondwana- Tropical Rainforest biome, dotted with mangroves due to plenty of rivers formed from snowmelt from mountains.
Himalayan Coast- Snowy and Frigid biome.
Antarctica- Extremely frigid and icy biome.