Restarting single flow does not work, restarts the whole instance

You are sending:

msg.headers['Node-RED-Deployment-Type'] = "reload";

Documentation describes:

The Node-RED-Deployment-Type header is used to define what type of deployment is performed.

full - all existing nodes are stopped before the new configuration is started. This is the default behaviour if the header is not provided.
nodes - only nodes that have been modified are stopped before the new configuration is applied.
flows - only flows that contain modified nodes are stopped before the new configuration is applied.
reload - the flows are reloaded from storage and all nodes are restarted (since Node-RED 0.12.2)

https://nodered.org/docs/api/admin/methods/post/flows/

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