I am only using this effect on a couple of the shots and actually only on the sky section and i will mask the sky so the effect only affects that area within the video.
Later on I was looking on Vimeo to see if their has been any infrared tim-lapses created and found this one by Philip Bloom a former Sky News cameraman who is now an independent filmmaker.
IR TIMELAPSE TEST from Philip Bloom extras on Vimeo.
This was shot on a Canon 5d mark 3 which has been specially adapted to shoot infrared.
While looking at this particular video I found a teaser for another timelapse he has done although the final version is not released at the time of writing.
Conversations from the 35th floor from Philip Bloom on Vimeo.
I like the tilt-shift effect used at the beginning of this video and would have liked to try something similar. This would require a tilt shift lens which are not cheap. Although I have seen ways to fake this effect I don't personally feel that they give a good enough result.
Below is the After Effects composition for the final shot of the video. Showing the masks and multiple layers used.
I have found this tutorial to try fixing flicker as the brightness change only affects one frame at a time so this may work. I am going try it when I get chance.
Die flicker! Die! How to remove that nasty high shutter speed/ high frame rate artefact in your NLE. from Philip Bloom Reviews & Tutorials on Vimeo.