I was able to stop the route finally. 
What I did was - 
1. set sendEmptyMessageWhenIdle=true in the file component. So when all
files from input folder are read and moved to backup folder, it sends empty
message.
2. On empty body, I am calling a processor.
3. And in processor, I am again checking if the folder is empty and then
using 
exchange.getContext().stopRoute("inputFiles", 5, TimeUnit.SECONDS);
to stop the route.

Now the route is stopped until the next scheduled time. :)

Thanks for your inputs.



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