To have your flowcharts appear in your project, export them by selecting:
File > Export > Export (*.json & *.uistate.json)
Save the two resulting files into the "flowcharts" folder of your project.
Then you MUST edit the "project.c3proj" file. In it, find this line:
"flowcharts": {
This line is usually at the bottom of the file (use search).
Then just add your flowchart name under "items", like this:
"items": [ "test_flowchart",
Save the changes. The flowchart will now appear in your project!
This works 100% – I actively use this editor in my own project.