Remember, there are two kustomization types. This page discusses the Flux kustomization type.

You can migrate an app between Flux kustomizations — that is, from being deployed by one kustomization to another — without any downtime.

Assume that an old-kustomization already exists, and has a path of /kubernasty/applications/oldlocation/someapp. Create a new-kustomization that has a path of /kubernasty/applications/newlocation if it doesn’t already exist.

old=old-kustomization
new=new-kustomization

# Suspend the old one so it doesn't apply any changes
flux suspend kustomization $old
# Prevent changes or deletions from tearing down resources
kubectl patch kustomization $old --type=merge -p '{"spec":{"prune":false}}'

Now move someapp from the old place to the new place, Make sure to delete references from the old place and add them in the new place. For instance, if there was oldlocation/kustomization.yaml that referenced someapp/some-resources.yaml, delete that there and put it in newlocation/kustomization.yaml.

Then:

git add .
git commit -m "Move someapp from oldlocation to newlocation"
git push

Watch the new-kustomization resource in Flux to see when it is fully reconciled with this change.

> k get kustomization -n flux-system new-kustomization
NAME                AGE   READY   STATUS
new-kustomization   57d   True    Applied revision: master@sha1:96a04a784ac7597d84f79bc9927b3e4f7557b106

Once that’s done, you can resume the old one. (It’s very important that the patch command was run previously.)

flux resume kustomization $old

This also works if you just want to delete the old one.