Same Problem today after "sudo apt upgrade" => from Thunderbird 52 to 60.2.1 
(64-bit)
In all my 3 Profiles Lightning had stopped working / disappeared. 
The First Profile had Lightning 5.4 installed as Add-On and now showed: 
incompatible .. deaktivated
Second and third Profile: In the Past, Lightning had been automatically 
integrated by clicking "keep it" and now it had disappeared.
Trying to install via search Add-Ons in Thunderbird only led to the 
incompatible 5.4.

Also NOT helpful was:
https://support.mozilla.org/en-US/kb/calendar-updates-issues-thunderbird
(Entry in Config did not exist at all)

There was also no change, when i started Ubuntu-Languages or so (DE:
Sprachen) and let install additional Language-Packages including one for
Thunderbird-EN automatically. (DE, which i use, did not show up as
missing).

What then helped in all 3 Profiles, was the manual Download and Install of a 
Lightning-Beta-XPI into Thunderbird:
https://archive.mozilla.org/pub/calendar/lightning/candidates/6.2b6-candidates/build1/linux-x86_64/lightning-6.2b6.de.xpi

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https://bugs.launchpad.net/bugs/1797945

Title:
  Lightning incompatible with Thunderbird 60.2.1

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