flat file vs db table

Our application is used to create records per department. On a specific day each department is verified and the data needs to be place into a file. At the end of the day the file is FTP'd to a mainframe.

Which of the following approaches would be better and why?

Create a file per department when it is verified, and at the end of the day merge the files into one and send it to the mainframe

                OR

Insert the data into a table (also contains indexes) when the department is verified and at the end of the day create a file with all the data.

Note: departments can be verified concurrently. Consider time take to perform the process as well.

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