I solved this for my case.
It was a conflict with my anti-virus.
Using Godot v2.1.4
Using antivirus Clam Sentinel,
which constantly investigates new files & system changes.
I had a similar error for C:/Users/User/AppData/Roaming/Godot/ (different files)
where it was
"Unable to write to file '(C:/.../project path/scene.tscn)', file in
use, locked or lacking permissions".
In the Godot Console it said:
"ERROR: FileAccessWindows::close: Condition ' rename_error ' is true.
When my anti-virus scans a file, it opens (or maybe locks) the file momentarily,
then closes it.
When I tried to save --and Godot needed to overwrite these files--
it was unable to, since my anti-virus had them opened in the background to scan.
My solution was:
I went into my anti-virus settings
+ set it to not live/actively scan the following directories:
 C:/.../path with my Godot project files/*
Clam Sentinel syntax note:
If you don't put the /* at the end of the folder path,
it will skip that folder, but it WILL scan subfolders.
The /* just means, apply rule to this folder, and all subfolders.
No more errors : )
I'm not sure how safe this is.