Saving in plugin?

I need some clarification on how saving works in the AE plugin. With the plugin interface open, File-Save Project seems to create a .autosave file. Does this just save the latest tracking, then you have to save the AE project as well to retain this update?

You need to save Mocha and close it, and then save the AE project to have the plugin data saved into your project. So it’s a two step process, save in Mocha, save in AE. Autosave is to recover from crashes.