It's Windows who relocate your files, not LibreCAD.
It is not recommend to store documents in Program Files folder.
I think UAC started with Windows Vista and since then access to Program Files and other system folders is read-only for regular users. You have to use administrator privileges to get write permission to these folders.
But it is
not recommend to run LibreCAD with administrator privileges to bypass this behavior.
So what you have found is the shadow copy Windows creates for compatibility reasons.
When a program with regular user permissions writes to any file under Program Files, Windows creates a copy and save changes in the user folder.
This happens transparent, so the file open dialog should find the files when you navigate to Program Files folder. But inside Windows Explorer this mechanism is not active and you don't find the files where you expect them.
So best solution is to change the default folder to any location in your users document folder.
Same applies also to libraries, templates and folders you need write permission.
Concerning libraries, you can keep those installed with LibreCAD in Program Files folder, but add a path in Application Preferences in your user space for new or modified libraries. You should see folders from both locations in the library browser then.
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