That's right, although for a support pack update, I'm not sure if the jobs even get suspended. In the past, when doing this with SPAM, there was no shadow instance to worry about, so it wasn't an issue. In upgrades, when there typically is a shadow instance, things are much more "shut down" in the system (jobs suspended, etc) than is often the case with support pack updates (though perhaps those should be just as much "shut down").
So in future I will definitely keep an eye out for it. Stopping the data supplier should be added to the tool and/or listed as a manual step in the guide to prevent inconsistent landscape and software component data from being replicated (or perhaps it already is and I missed it). I'm going to tag Boris Rubarth to get his take on it, as he is a key player in the development and maintenance of the SUM tool.
Deleting the extra instance in SLD was very easy, and I watched it replicate to LMDB very quickly, and it immediately disappeared upon refresh from the managed system configuration tool. However, it later showed up in diagnostics agent administration, as well, as a warning about a system path not being reachable by the agent (it was trying to reach \usr\sap\SID\DVEBMGS03, which doesn't exist), and so I had to edit the agent landscape paths to remove that as well).
Although the problem is long since solved in my system, as described above, I will keep the question open for a few more hours to see what Boris or others may have to add.
Regards,
Matt