You need to give more information on what is actually happening. For example when you say:
1. "because as soon as i execute the above method then i am not able to read the updated file(outputFile)" how are you trying to read the updated file?
2. "however after update the file if i open the file manually then i am able to read the file programmaticaly" what do you mean by open the file manually? Have you tried closing and restarting the application and can you read the file then?
Are there any exceptions thrown when you try to read the file after updating it?
You haven't shown the calling code so make sure it isn't catching and discarding any exceptions that might hide the cause of the problem.
BTW when using streams
you should always close the stream in a finally clause of a try-catch statement.