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When making patch groups you can make an exclude group (skip selected), or an include group (scan selected). When you create an include group those patches are the only items that will be scanned for, so you can just leave out the items you would like to avoid and it will not show them missing.
When creating an exclude group it will scan for all items selected under other filters, except the patches you have placed in this group.
There is also the option of scanning for any missing patches and only deploying selected patches from the scan result. Just shift/control-select the patches you would like and right click and deploy selected patches.
Below is a video for creating patch groups if needed: