C++ classes in Content Browser is just for blueprint only users, more naturally you should use Class viewer in Window->Devlopment Tools->Class Viewer, it hsows class in inherence tree, blueprints included. You cna not change organization in content browser, because C++ classes are just virtual assets created on runtime, while other assets are uassets files which can be moved.
VS project is not needed for compilation, it only exist for you to open end edit files, it get regenerated if you right click uproject file and generate them, also class wizard in editor will trigger regeneration of project files. With regeneration all configuration in project gets overwritten back to default settings, thats why it resets.
There only 2 ways to organize cod filese:
Stack them up in Source and module folder like default it does
Make Public and Private folder inside it, Public should have header files that will be exposed outside of module, private should have all cpp files and header files to classes not exposed to outside of the module
Simply close everything, go to file explorer, make your sub folders and move files arround.
Here some exemple of folders i use
Dynamics
traps
logic
gameplay
Units
player
enemies
UI
Menus
HUD
Wolrd
Special(thing that extend some pluggings)
User (profiles/option)
Then right click on your upluggin file and select regenerate vs files
Open vs solution and try to rebuild => it will fail
Fix all includes as you moved files ( thats why there is no “drag &drop” in UE/vs )