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This seems to be the issue: https://github.com/rancher/rancher/issues/35717
The relevant UI code is https://github.com/rancher/dashboard/blob/master/pages/c/_cluster/apps/charts/install.vue .
I rearranged values in an array, then the next time I tried to upgrade Rancher incorrectly applied the values to the wrong array items leading to an invalid application deployment. From a user's perspective this looks like Rancher is corrupting the values. All of this was done on the Prometheus helm chart.
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