Seems update 52.0 makes some changes to the lightning extension. Lightning should now be a built-in extension with thunderbird, but doesn't appear to have happened. Updating makes the extension incompatible. There is apparently a way to fix it by making a new profile and moving the extension manually to that profile, didn't try this. I tried deleting my profile and reinstalling, but lightning was nowhere to be found.
An update to the Arch Package seems to have fixed this for Arch users here - https://bbs.archlinux.org/viewtopic.php?id=224903&p=2