In my case with a Galaxy Note 2, already rooted and with ClockWorkMod recovery installed, after flashing to CM12 and install Gapps 5 (and selecting the option while in recovery to restore root) I still lost root.
To re-enable root, go to Setting>About Phone>and tap Build Number 7 times. That will unlock Developer Options. Then open Developer Options and the option is there to enable root access. Once that is done you can then reinstall apps like SuperSU.
Also, if you were backing up data to your external SD card (ex: I was using Titanium Backup) the path changes under Lollipop. So if it says it cannot find your data, you need to update the path. For example my path changed from extSDCard to SDCard1.