You likely deleted the MDF file in Windows Explorer. SQL Server LocalDb doesn't know about it and the error is probably complaining about not being able to locate the MDF file.
To delete it properly, you can delete the database from SQL Server Management Studio or SQL Server Object Explorer in Visual Studio.
Alternatively, you could have selected "Show All Files" in Visual Studio Solution Explorer, located the MDF file in App_Data, right-clicked to delete it from within Solution Explorer itself. Visual Studio seems to do the right thing and let SQL Server know about this change.