MPC projects and plugin settings are saved seperately.
If you select a factory preset for your plugin and make changes to its settings, then you save only the MPC project itself without seperately saving the plugin state, the changes that you made to the plugin will revert back to it's factory preset state when you reload the project.
To avoid reverting the changes you made to the factory preset of your plugin, you will need to click the Save button in the top section of the plugin window, create a name for your new plugin state, and click Save.
The next time you save and reload your project, the plugin save state will load in conjunction with the project.