Symlinks not updated until php5-fpm isn't killed and restarted
As per your php -i info I think your servers have opcache enabled on the fpm side, not though command line. This is why it shows opcode.enabled
You can try to force a cache clearing of opcode just after your symlinks are recreated. You need to run this on a script that will run under the same php-fpm process. i.e. create a page that does just a cache reset
http://php.net/manual/en/function.opcache-reset.php
And call the page using wget/curl/browser, dont just run the php file from the command line as the command line will not be running on the same process pool where the cache has been created into.
Also if you are interested in a more flexible tool to clear cache use https://github.com/gordalina/cachetool
Pls let me know if it fixes your problems