Use an Activate Procedure. Activate procedures are designed to be run multiple times on an agent without creating install records. An Install procedure needs to be run on the agent first, then a Activate procedure can be run as many times as needed without having to check the "Remove installation records and re-run the selected procedures" Box.
To create the activate procedure right click on Procedures and select New - Added Procedure:
Give the procedure and name and select Activate for the Task:
Click the Embedded File Tab and Enter the File you want to run and enter the folder the file is in for Subpath:
Seal the package and send the Install Procedure first, then the Activate procedure can be sent as many times as needed.