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Revised updates are not syncing to SCCM

Creating custom updates with Patch Manager and then syncing them to a SCCM environment. After making the changes and selecting the options "Re-sign existing selected packages" and "Delete package if it exists (select this if binaries have changed)" in the publishing wizard the publishing process reports that it published to the WSUS server correctly. However, when I do a software updates sync in SCCM, any meta data changes about the update appear to change, but the content location and the actual download has the old path and cab file. If I look on the WSUS Content folder, I can see the new content is there. I can also find the old content, so it appears that it never deletes the old content.

How can I successfully change a custom update if testing failed and we needed to revise the installer?