I only recently started using Folder as Workspace, but I haven’t seen that. When I have launched an external process which affects the files in the folder that’s viewed in FaW panel (compiler or similar), I can see a brief flicker as it creates then deletes temporary files… but I’ve never seen it show multiple copies of the same file in the FaW list.
However, Code::Blocks is more than a compiler; from what I remember when I played around with it a few years ago, it’s an IDE (editor+debugger) which references a compiler (and you can actually choose between different compilers at installation time or through configurations or something). But as an IDE with powerful editor features, maybe something that it is doing is interfering with the way that Notepad++ tries to monitor the folder. I’m not sure how well you’re going to be able to mix NPP and C::B.
But it might be that some of the Settings > Preferences > MISC page will help – specifically, the File Status Auto-Detection. But folder contents aren’t the same as file contents, so maybe those settings won’t affect it.