On each Publishing Service sync, Patch My PC queries the SCCM DB to see what applications are installed on workstations. Can an option be added to "uncheck" updates from the list of updates and/or applications in the PMP Publishing Service settings that were originally enabled by the PMP auto-publishing rules so those applications and their updates are no longer published?
This will help prevent storage on the WSUS server and server/shares used for SCCM source content from being filled by updates and applications no longer needed. Additionally, since it would no longer be checked, it'd also reduce the time the Publishing Service sync takes to complete.