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I deleted the system-upgraded-controller deployment, uncordoned the one node, and removed the labels from the other 2 nodes. So far I think everything is working ok

Did you import this cluster into Rancher, or did you at some point deploy the SUC manually? If you’re using the SUC, normally you wouldn’t go update the binaries by hand…

This is the local cluster where I installed Rancher, I didn't explicitly import it into Rancher but it's in there, so I'm assuming that Rancher does that automatically when you first deploy Rancher in the local cluster? My other clusters are built exactly the same and do not have the SUC deployed, so I must have done it manually back when I was first getting all of this working. I didn't even realize it was deployed which is why I was manually updating the binaries. The manual binary update is so simple we plan on just doing that and not worrying about the SUC especially in the air-gapped environment. It seems to be working fine so I think just deleting the SUC deployment is ok.