You cannot overwrite the data in an excel worksheet with

the functionalities offered by SSIS to manipulate excel file.

I will suggest you include a cleanup process in the application

that uses the data in the excel file that will either delete

the file or rename it when done with the data.

If the data in the excel file is used by another SSIS package, then you can

include a File system task in the package to do the cleanup.

Cheers!