In some circumstances, a patch or update to software may require the original install source to properly apply. After Software is delivered to a system if the software was published directly to the portal, and not by a Managed Delivery Policy, the source files are cleaned up (deleted).
This is working as designed. When a task or policy no longer applies to a system, the files are deleted, by default, after one week. The portal cleans up unused portal tasks after 15 days, so an estimate of 22 days after the software is delivered the downloaded install files will be deleted.
In those rare cases where the source files need to remain, use the following method to keep them on the computers.
This setup will ensure the package gets downloaded, and that the execution does nothing. Because the policy is active, it will keep the package downloaded until the policy is disabled at some future date.