I believe your question is related to both the Stories aren't saving on Windows with relocated User directory issue #340 and the Story Library Location Issue #389 on the Twine 2 project repository.
Unfortunately the code that decides where the "(My) Documents" folder is located on each Operating System currently makes assumptions that are not correct if the user has moved theirs using Windows's built-in ability to do so.
There is currently no simple built-in way for end-user to move the location of the Twine > Stories folder, and the method of using a HOME environment variable to trick the application into thinking it was running on a non Windows machine no longer works.
There have been a couple of different suggestions (see request #106 Ability to change the story directory path [wip] and request #108 Desktop app file system paradigm for NW story files) on how to implement a possible solution to this issue but they needed to be halted due to the restructure/redesign of the application that became v2.1.0 (from memory)
NOTE: One semi-complex method (trick) that still works is to run the application so that it creates its Stories folder where it wants to, and then to replace the Stories folder with a Symbolic Link to the actual location you want the story project files to to be stored in.
This is how I control my own environment so I can have one location where I store all the projects I need to create when answering other peoples questions and another location where I story my own projects.