How do I check in deleted files and folders at the root of a sandbox using the CLI?

Thanks for the feedback. Just to be clear are you saying that if I specify the root directory to be the sandbox location e.g. 'scm checkin -d c:\sandbox1 c:\sandbox1 ...'. then 4.0.5 now detects root level deleted files and folders (unlike my current version 4.0.3 which does nothing for the same command)?

In your example, you would actually want to pass the root directory of your project inside your sandbox. For example -
scm checkin -d c:\sandbox1 c:\sandbox1\project1 ...

My query is about checking in deleted files and folders that were at the root of the sandbox i.e. they have no parent folder. The root files and folders have been deleted and I cannot checkin their parent folder as usual because the deleted files and folders were already at the root of the sandbox. As I detailed in my question above I used the CLI command 'scm share <workspace> <component> <directory*> -r <repository>' i.e. '<directory>*' to check in top level files and folders to the sandbox root as I do not want these files and folders to be in a top-level folder.

If I understand your question correctly, you ran the share command to add files/folders into your component. Example -
scm share  -r <repository> -u <user> -P <password> <workspace> <component> <path>
If the value of "path" was c:\temp\component-x, then the command above will automatically create your sandbox at c:\temp.
Now, you decide to undo the share operation. So you first delete files/folders (C:\temp\component-x and everything underneath) and then run this checkin command-
scm checkin -d c:\temp c:\temp\component-x -u <user> -P <password>

I still don't see how I checkin a deleted root file or folder. For example I share a file at the root of the sandbox 'c:\temp' using 'scm share <workspace> <component> c:\temp\file1.txt'. Later I delete the file and 'scm status' shows the file as 'd--' in the unresolved section. I now want to checkin this deleted file - how do I do that?