Unless you tell the service to run node-red with command line parameters, it will NOT be using that folder.
You have two choices...
- create account "node-red" and run the service under that account - you will see that it creates
C:\Users\node-red\.node-red\settings.js
on first run - add command line parameters to tell the service to use the folder
C:\Users\jon\.node-red
The docs tell you what the command line parameters are (or run node-red --help)...
C:\Users\xxxxx>node-red --help
Node-RED v2.0.5
Usage: node-red [-v] [-?] [--settings settings.js] [--userDir DIR]
[--port PORT] [--title TITLE] [--safe] [flows.json]
node-red admin <command> [args] [-?] [--userDir DIR] [--json]
Options:
-p, --port PORT port to listen on
-s, --settings FILE use specified settings file
--title TITLE process window title
-u, --userDir DIR use specified user directory
-v, --verbose enable verbose output
--safe enable safe mode
-D, --define X=Y overwrite value in settings file
-?, --help show this help
admin <command> run an admin command
Documentation can be found at http://nodered.org
e.g. set your service to run node-red -u C:\Users\jon\.node-red