Thank you guyz, because I had to find the solution I searched alot on the internet and finally found Tinderbox DeFlicker. Great plugin for AE. Simple settings and the result was perfect. After reading david’s reply I was planning for a reshot. But with the help of DeFlicker everything is constant now. No frame based settings, no segmented layers. Clean and simple.
There is also another great plugin called GBDeflicker which is ideal for timelapse footage. Though GBDeflicker didn’t work for me but still I belive a good plugin.
Thanks again for the help.