Not the first time I ran in the problem that the .ssh folder in Windows changed from the .ssh of the specific user folder to the folder of the Git installation. Now I tried to investigate what actually causes the problem.

I was able to verify that the presence of the binaries of the Git installation in the Windows PATH was responsible for the problem, e.g. C:\Program Files (x86)\Git\bin. Unfortunately, I wasn’t able to solve or understand it, but I suggest a better way to get around the problem. Furthermore, the problem also affects only the Windows command line but not Git tools like SourceTree.

Although the simplest solution is just to copy the .ssh folder so that consequently 2 ssh key locations exist, I suggest to create a symbolic link on Windows by executing mklink /D your_git_installation_path/.ssh your_user_folder\.ssh which allows you to avoid the redundancy of two same folders.