Autostart is controlled by the systemctl service file /lib/systemd/system/nodered.service that is created by the pi install script. By default it runs node-red as the user that ran the install script so it will pick up the flow from that users .node-red directory. If you run
node-red-stop
node-red-start
it will stop and restart node-red using the service file and you will see in the terminal which flow file it runs.
You should be also be able to find the name of the flow by opening a terminal window and doing a cd .node-red and then a 'ls -al *.flow which should show you the name of the flow.
To add to all the valuable answers you've already had, here are some more details.
As has been said, by default Node-RED will use ~/.node-red/flows_<hostname>.json.
You can change that in a number of ways:
by specifying the file you want to use on the command line - https://nodered.org/docs/getting-started/running#command-line-usage.
This approach isn't really suitable if you're running as a service on the Pi as it would require you to edit the service definition file - which would get overwritten when you upgraded.
by setting the flowFile property in your settings file (~/.node-red/settings.js)
Node-RED actually creates two files for your flow; flows_<hostname>.json contains your flow configuration and flows_<hostname>_cred.json contains any credentials your flow uses.