Pavlovia syncing works via Git, which is a system for tracking changes to a folder. When you click sync, it look in the “Project Root” folder for files which have changed and sends those changes to Pavlovia. Those “untracked files” are files which, somehow, the project has been set up to ignore. If you set your file browser app (Finder on Mac, Explorer on Windows) to show hidden files, you’ll be able to see a folder called .git in the project root folder - within that should be a file called .gitignore. If you open that in your preferred text editor, what does it say?