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i think you are going to need to upgrade to an air gap type install and use a registry. https://docs.rke2.io/install/airgap

I'm not sure if it's really necessary to use an air gap type install. We have imported the Root CA certificate that will also be used to decrypt and re-encrypt the traffic. Theoretically, we just to need to upgrade Rancher to a new version for example and just omit the proxy variables. But is this supported?

if it's a transparent proxy and everything happens magically. it's possible. but i'm not really familar with what is being used to update. you might be able to work out something with the noproxy options to allow the proxy for the updates and not sue the proxy for mainstream traffic. https://docs.rke2.io/advanced