Persist changes to Live YAML deployments

Question from today:

Hi, We have a situation where for some of our airgap customers because of some unique local setups, we had to patch our deployment yamls on the fly to make it work. The problem however is that when kotsadm gets rescheduled to a different node (they rotate VMs or suspend/resume) it overrides any patch update. Is there a way to make these yaml updates stick with kots ? These arent image fixes but some local changes which we want to stick until we give the next airgap.

The Patching with Kustomize | Replicated Docs feature may be able to help with this.