My repository in git looks like this:
-Project Repo
-Sub Folder 1
-File 1
-File A
-Sub Folder 2
-SubSub Folder
Hopefully a symbolic link is all you need.
If you are in Linux/Unix you would issue the symlink creation command as follows:
cd ".../Project Repo/Sub Folder 2/"
ln -s "../Sub Folder 1/File 1" "File 2"
In a version of Windows that support symbolic links, you can try the mklink command:
cd ...\Project Repo\Sub Folder 2
mklink "File 2" "..\Sub Folder 1\File 1"