### Godot version

4.0.dev.d1e5903c67956707948b1de370b807e3aad395b7

### System information

macOS 13.1

### Issue description

Script classes are not regenerated project-wide after first import. See the reproduction steps below.

This is a huge problem for large games since a class may not have all of its dependencies ready by the time it comes to parsing the script, so it doesn't get registered on the first pass, and there are no other passes. The only solution is to manually open every single script and save it (potentially multiple times if there are long dependency chains).

The symptom is happening as of #70557, but the root cause was still present before that PR. If I revert that PR, open the reproduction project, and then instead of deleting the below file I empty out the `_global_script_class*` members, A and B do not regenerate (but they do if you open and save them). This has become a serious regression because the class list is no longer saved to version control, so you can end up in a situation where deleting `.godot/` results in a broken project until you manually open and save every script (for every developer, every time they delete `.godot/`).

### Steps to reproduce

1. Download an open the below minimal reproduction project.
2. Look at the generated `.godot/global_script_class_cache.cfg` file. Both A and B will be in there (good).
3. Close Godot and delete this file.
4. Open Godot again.
5. Look at the lack of a `.godot/global_script_class_cache.cfg` file. It is not regenerated (bad).
6. Open the `a.gd` script and save it.
7. Look at the generated `.godot/global_script_class_cache.cfg` file. Only A will be in there, but B will not (bad).

### Minimal reproduction project

[GlobalClassMissing.zip](https://github.com/godotengine/godot/files/10515105/GlobalClassMissing.zip)

template <typename T>
class TypedArray;
typedef void (*ScriptEditRequestFunction)(const String &p_path);
class ScriptServer {
	enum {
		MAX_LANGUAGES = 16
	};
	static ScriptLanguage *_languages[MAX_LANGUAGES];
	static int _language_count;
	static bool scripting_enabled;
	static bool reload_scripts_on_save;
	static bool languages_finished;
	struct GlobalScriptClass {
		StringName language;
		String path;
		StringName base;
	};
	static HashMap<StringName, GlobalScriptClass> global_classes;
	static HashMap<StringName, Vector<StringName>> inheriters_cache;
	static bool inheriters_cache_dirty;
public:
	static ScriptEditRequestFunction edit_request_func;
	static void set_scripting_enabled(bool p_enabled);
	static bool is_scripting_enabled();
	_FORCE_INLINE_ static int get_language_count() { return _language_count; }