The noise in that animation clip is only in the clouds, as far as I can tell, and they are probably v3 clouds. v3 cloud GI quality (and thus likelihood of flickering) is controlled separately from primary GI (in the Cloud GI tab), and is not fully cacheable at this time. You need to use higher Cloud GI quality settings to avoid this. Reducing detail won't help with that issue, unfortunately.
As for why noise issues get worse at sunset, it's because you're dealing with a much higher proportion of indirect light, which is more diffuse, so you need more samples to reach an equivalent level of quality/noise. This is virtually unavoidable in a realistic light simulation. However, looking at your .tgd, I think there are some good ways to optimize your settings.
First and foremost, I strongly recommend reducing Micropoly Detail below 0.9 (also Ulco also noted). Micropoly Detail is only going to affect the detail of your terrain, not your clouds or atmosphere, and not your objects (trees, etc.). Since your terrain is almost entirely covered by trees here, you will see virtually no difference between say 0.6 or 0.7 Micropoly Detail and 0.9 as you have it set here. So I would recommend trying 0.6 first and do a short frame sequence and if it's not quite enough detail *in the exposed terrain parts*, then try 0.7. You really should not need more than that though. And this will save you some render time.
I also recommend not using 3D Motion Blur here. You'll see minimal blur at this altitude and speed, but some additional samples may still be calculated for it, to minimal beneficial effect. If necessary use 2D motion blur, either in Terragen, or in another package.
Since you are using AA8 and are ray tracing the atmosphere ("defer"), I would also suggest reducing the atmosphere samples quite a lot. 16 ought to be fine with AA8, or at most 24, even for the dusk shot. If you are using higher atmosphere samples for the daytime shot you should definitely be able to use only around 8-12 samples with an AA of 8. AA8 is quite high and should be sampling the atmosphere very well. You should also strongly consider whether you need the "Receive shadows from surfaces" setting. Only keep it enabled if you see shadows *in your atmosphere* (*not* onto clouds) that you want to keep. I would suggest trying a test frame of the sunset scene with it disabled and see if it makes a difference. I do see there is an area with somewhat subtle rays coming off a terrain element right in the middle of frame, so it may be worth it to you to keep it.
Also consider whether your higher Cumulus clouds (Layer 01) actually need Receive Shadows enabled. This should only be for shadows *from* the terrain, and they seem too high up to receive any shadows from the terrain here. With the setting disabled they'll still get shadows from other cloud layers. It may change the lighting slightly, but should not have a dramatic effect and will save render time.
For all cloud layers you can consider/test using "Conservative Acceleration" in the Acceleration Cache (on Optimization tab). It may take you some hours to test all this, but if you can reduce render times per frame by 50% or more (likely, if you test all the above), then you will have saved yourself hundreds of hours of render time.
I also see you have 360 degree detail enabled here, and set to "Highest" rather than "Optimal". This may be your biggest potential source of render time savings. I'm not sure if you are using this just because of the problem you had previously in a different (though somewhat similar) scene, or if you actually tested in this scene to make sure it's necessary, but if you have not tested you definitely should. Test first with Detail in Crop, and then try some amount of non-360 padding or "Optimal" 360 padding if you see any issues.
The reason this may be a very different case than your other scene is that you are facing into the sun here (at least later in the animation), and so shadows are being cast in most cases from *visible terrain geometry*, i.e. terrain that is already being handled by the main render process for the primary view. The need for Ray Detail Region Padding depends almost entirely on any shadows cast from *off-camera* geometry. Such shadows will vary tremendously, even for the same sun altitudes, depending on camera angle relative to sun angle. So again, if you are seeing the terrain from which shadows are cast, the shadows will be correct, it's only when shadows are coming from off-camera geometry that you need the region padding. Turning this setting down or off can save you a lot of render time.
I would also note that turning off Ray Detail entirely ("No Detail") saves a huge amount of render time, at the expense of most of those rays in the atmosphere coming off that center-frame area of terrain. If that subtle detail is not vital to your quality of output, then you can get frame render times down to less than a 10th of what it was, however it does produce differences in the final output so do test it first to see if it's acceptable.
Attached is an optimized TGD that cuts render time in half.
- Oshyan