Hi,
Sorry for refreshing old thread, but I have the same issue with symbolic links. I have 2 Moodle installations on localhost connected to 2 different databases. And I want to symlink a directory (let's say it will be specified theme directory) from one Moodle to another. My server is running on Apache, I used ln command and ls -la says it's linked, but second Moodle doesn't see this theme - it doesn't see that new theme folder was "added". Of course theme is working fine on first Moodle. I edited /lib/moodle.lib like Mathieu Petit-Clair adviced but it's not working for me. I even tried to force new theme by setting it manually in database, but it also didn't work. Has anyone fixed such issue?