Many thanks Nicholas, works perfectly. Just as a reference for anyone with similar needs this is a suitable curl:
curl -X POST -d @userdir/
flow.js.new http://localhost:1880/flows -H "Content-type: application/json" -H "Node-RED-Deployment-Type: full"
given that the command is issued inside the same host running nodered, the updated/modified flow file is userdir/
flow.js.new (relative from currend folder) and no auth is needed from localhost.
The command can be part of a shell script that (example) pulls with git a new flow file, or watches for a file being modified by a mqtt sub pending... full example coming soon on github!
S