Actually, you just need to export the plugin as is, and when you load the project folder again, it will load your settings directly from the plugin and you won't lose anything.
The details of this are at the end of the second paragraph of the documentation.
But since I like to simplify things for my users, I've added an option for you to save the project, in case you're working on a prototype and don't want to overwrite your project. Furthermore, once the project is loaded, when you ask to load the folder, it will search for files that have been modified after the project was opened and only load the images, maps, and other supplementary information.
Please download file 2.1 and proceed with the tests. I truly hope this solves your problems.