quick reboot never works [for me]
recreate mount scripts almost always works [for me]
Whenever you do a rom update, and see link 2 sd not working. Don't panic, your apps are still there. Only the apps that were moved as a system app will be gone.
(If you even chose to do that. For example I had go launcher moved as a system app instead of being linked as its a launcher. I also wanted the system to accept it as part of the system, mainly because I saw a performance increase compared to just leaving it on there as a standard app.)
I have always done the following:
open link 2 sd. Disable auto link for new installed apps, disable the link at boot option. Restart the rom several times. After 3 or 4 restarts of the rom, open link 2 sd back up. Recheck all your settings. Then restart again. If you are still getting mount errors or any other error, recreate mount scripts. If you get an error, try going through choosing different file systems
(ext, fat32) until you get the message that link 2 sd will create the mount script at boot and prompt you to restart. After doing the recreate mount scripts, do a quick reboot. It might take a very very long time. It took mine 10 minutes before It booted up. After it boots, let it sit some more at the home screen. Restart the entire phone again at least a couple more times. You should now be fine.
That's the entire process I did to make everything work again after the rom update.
I would also suggest after everything is working properly, to go into link 2 sd and clean up the 2nd partition as well as dalvic cache, clear all app caches, and last but not least link dalvik cache files. Then choose the refresh option and reboot. Should also gain some more space that way.