I don't know how Thunderbird gets into that state. Lightning comes with a version matched to the current version of Thunderbird. If you do a clean install then Lightning is included and it just works. If you update, it should check for updates for add-ons and just automatically fetch the updated version of Lightning. Where it does tend to fall over is when Thunderbird is downgraded. In these cases, I'd uninstall Lightning, go to the Lightning versions page and manually download and install the appropriate version.

https://addons.mozilla.org/en-US/thunderbird/addon/lightning/versions/

As an afterthought, if you also use the Provider For Google Calendar addon, you need to keep that at the right version too.

I have the same issue, every time i update Thunderbird on Xubuntu. I don't understand how they can say that lightning is integrated, it clearly is not.

I even went as far as an entire clean install of my system with a fresh thunderbird and everything, result. 1st update disables lightning again.

This time i had to downgrade lightning (which was 6.1b1, as installed by thunderbird itself) to 5.4 ?!?!?

I love how almost every answer is, type lightning in extension search bar and install it, it doesn't even show up there anymore :) I had to use the url from this question to get the right version.