The pegasi city is too high to be Canterlot, and there is not a mountain top in the solitary image we have of Zephyr Heights. In the G4 show, cloud banks around the mountain top on the nameless mountain were constantly seen high above Canterlot. Then it means that when the pegasi took over, they removed the mountain top and built a city there far above Canterlot. As the G4 show has shown the city from different angles, we know that it is located on a plateau where a stream flows from several waterfalls, and that the mountain itself is part of a ridge at the end of a local mountain range. From the G4 map we know that the Foal mountains are to the west, and from the S9 we know that the Rambling Rock Ridge is at the same height as Canterlot.
The mountain did not stand alone, it lies as part of a mountain plateau with lower land in all directions with many mountains and heights, which seemed to be at 600 to 1,000 m above sea level, and probably 300 to 400 m above Ponyville which lies at the bottom of a valley floor. The mountain plateau can thus have many different names divided into geographical features. The actual mountain that Canterlot is facing, seemed to be about 2,000 m high, as the tree line seemed to end probably about 150 m above the city itself. Then it meant that Canterlot is 900 m above sea level. As many high peaks and mountain peaks have snow, this means that these are in the “alpine climate” zone, which is usually 1,000 m to 2,000 m high. And from the show it seems that the mountain did not stick up alone, from S2 it has been discovered that there are “neighboring mountain peaks” to the east and northeast.
Zephyr Heights was probably not the name of the pegasi capital or of the mountain itself, but of the heights at one end of the mountain plateau that include the Ramling Rock Ridge (which may be the road Sunny and Izzy took when they were stopped by the pegasi) - with the dry stone surroundings as seen in the first recording of Zippy. Since Sunny and Izzy had come from the southeast, it would be logical that they went up on the Ramling Rock Ridge. From there they can look down on the Everfree valley and towards the White Tails Woods in the distance.
It is possible that Canterlot was abandoned or reduced to a small suburb, while the pegasi began to build its new city of 1,800 to 2,000 m, by removing the mountain top and connecting this with the other mountain peaks. As there are many tunnels and mine shafts through the mountain area around Canterlot, the pegasi can build the city from within the mountain itself. A bonus with this is being able to look down on Canterlot from very high up, the pegasi can become jerks if they want to. But it can have consequences for the valley below them, too much of the meltwater from the snow-capped mountain peaks may have either been lost or redirected, so it may be very different where Everfree and Ponyville are located. It is possible that the lake below Canterlot, Saddle Lake, which is important downstream, has disappeared.
But I do not think it has had consequences for agriculture in the valley, because without the earth ponies and they can not be too deeply dependent on outside food producers, it means that the pegasi must have had agricultural workers who could continue to grow food plants on the cultural landscape. A big city must have food. Lots of food. But; Ponyville by being downstream can lose its value as a food production site, and can be abandoned as a consequence. The practical earth ponies will go away rather than stay if the water is absent from their fields or if their village is flooded by a new river course.
I think Everfree will be intact, and that it has assimilated both the castle after Twilight and the Treehouse of Harmony, and remain a dangerous place. For not all magic is gone; it seems that a minimum of background magic is intact, and the crystals in Izzy`s home can be a solid indication that stored magic can survive in intact crystals. This may mean that the Crystal Empire may have survived, and that magical beings with internal magic - such as dragons - will not die out after the magic has disappeared. I see that many have now seen what the consequences of absence of magic can mean. It was a very bad idea to let the magic disappear without thinking about the consequences, when the script for the movie is being prepared.
In my headcanon, it’s possible that Everfree was where Tambleon once lay, when Grogar ruled before Gusty the Great rebelled against him. And then it meant that the magic of Everfree will not disappear so easily, but the unicorns will definitely refuse to have anything to do with something so dangerous. They probably prefer places where they can find stored magic, but the road to Crystal Empire will probably be blocked by ice and snow, just like when the Mane 6 got there for the first time.
