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I've never had Pulumi remove my comments.  Are you using the automation API by chance?

As far as I know, Pulumi stack configuration is tightly-coupled with these YAML files.  To the point that the CLI and Automation API which wraps the CLI require them.

<https://github.com/pulumi/pulumi/blob/master/sdk/nodejs/automation/localWorkspace.ts#L31-L43>

I'm not using the automation api directly, but the file is overwritten/reserialised on each pulumi preview or pulumi up - so I guess something could be going on with that automation api

We'd need to see more code to make a determination.  The stripping on the comments in the Pulumi stack configurations is not something I've ever had happen.

It seems I'm running into specifically this: <https://github.com/pulumi/pulumi/issues/6848|https://github.com/pulumi/pulumi/issues/6848>
Which would be addressed by this age old issue: <https://github.com/pulumi/pulumi/issues/423|https://github.com/pulumi/pulumi/issues/423>