Xcode Project Files not appearing in Project Navigator

May be you need check the Project Navigator's bottom, there is a search bar.

If the search bar had some keywords, the Project Navigator would only show the files which file's name contain the keyword(s), and you can't clear the keyword by only reopen Xcode.

When you open Xcode, Xcode will initial the search bar with nothing and you can see the complete files, after initial had done, Xcode will load last close time's state for the search bar and filter files, so that's why When I open my project, the files appear for about 1/2 a second.

Untick this timer icon at the bottom of navigator in case you have selected it

For me the issue was different. My search bar was empty but I had mistakenly selected the clock icon in the search bar at the bottom of the navigator.

Unselected it looks like this

Selected it look like this

The clock icon filters the files for files that have been recently used and therefore, hides a number of your files.