I have a use case where i want to read two excel files (say ex1 and ex2 ) and update data of ex2 on top of ex1.
Why would you need to do this in a tJavaFlex? You can use two tfileinputexcel components and a tMap to do this. The only thing that might slightly change your use case would be that you would have to write your data to a tHash component and in another subjob, carry out the updates the Excel file. This is because they don't like being read and written to at the same time....an Excel issue.
Agreed we can achieve this by using simple tMap. But i need to perform some business logic on particular subset of data on both the excels.
There is no reason why the business logic cannot be carried out in the tMap, but if you want to do this in a tJavaFlex I guess you can use these APIs https://poi.apache.org/. They will allow you to read and write to Excel files. However it will not be as easy (unless you are happy with writing Java) and will not be as clear to other Talend developers (unless they can read/write Java).