In this post, I'll show you how working with multiple layers fixed a severe flicker problem. The "key-frame shift method" is also a successful tool, and you can learn more about that one here.
A customer was having trouble de-flickering a time-lapse video and asked me have a look. His clip had some serious flickering of a kind I hadn't seen before. It was shot using a Nikon D7000 and Tokina 11-16mm f2.8 lens. Apparently, the lens iris was not operating smoothly, causing significant differences in exposure between frames and leading to a great deal of aperture flicker.
The flickering was so severe, GBDeflicker applied with its default settings couldn't fix it. But, I was able to get a good result by de-flickering the sky and foreground separately, and combining them together using a layer mask.
Watch this demo to see how I did it.