<p>I have a number of <code>.yml</code> files with deployments and their services and need to set <code>.spec.progressDeadlineSeconds</code> to all of them preferrably from one common place.</p>

noname7619
<p>I would recommend checking out <a href="https://kubectl.docs.kubernetes.io/references/kustomize/builtins/#field-name-commonannotations" rel="nofollow noreferrer">kustomize</a> for doing tasks like this. From the limited information it sounds like <code>commonAnnotations</code> might do the trick for your use case, but if not there are other transformers that could like <code>Patch</code> or <code>PatchStrategicMerge</code>.</p>
