It probably wasn't the rmdir command that deleted the parent folder by itself, but the LLM did the traversal. The LLM probably did this:

    rmdir D:\dir one\dir two\file

Detected that it failed, then the LLM issued the traversal command

    rmdir D:\dir one\dir two

And so on...

    rmdir D:\dir one

And then that failed, so...

    rmdir D:\