I am running Sublime Text Build 3113 on MacOS El Capitan.
I opened a folder with a larger project that contains several sym-linked folders.
Some folders in the side bar show a different symbol (folder with an arrow in it) and cannot be opened.
These are always folders for which a symbolic link exists. However, sometimes the physical folder behaves like this and sometimes the symbolic link.
My best guess would be that the first time a folder is encountered during indexing (be it the actual physical folder or the symlink), the folder becomes the actual folder for Sublime and all later encounters become the link.
Desired behavior:
No matter whether the folder is a physical folder or a symbolic link, one should be able to open it.
Okay behavior:
Do open the actual physical folders. Show the symbol for symbolic links.