Question Meta files not being edited

Hey, could really use some help on how to fix this but I have a annoying problem where when editing or deleting a file or folder from the Project Window (In the editor like normal) it gives me this error or simular every time.
I.E
A meta data file (.meta) exists but its folder 'Assets/VisualScript' can't be found, and has been created. Empty directories cannot be stored in version control, so it's assumed that the meta data file is for an empty directory in version control. When moving or deleting folders outside of Unity, please ensure that the corresponding .meta file is moved or deleted along with it.
UnityEngine.GUIUtilityrocessEvent (int,intptr,bool&)

Basically all I did is make a folder called "VisualScript" then right clicked in the project window where I made it and pressed delete. The file does not delete and also I get this message.

From this statement in the doc = Unity will also automatically move or rename the corresponding .meta file
This is not happening for me, but only occurrs on this project all other work fine. any help would be great its just annoying going to file explorer and doing it all in there.

Thanks