Updated PureOS 9 through apt, it included the latest version of Thunderbird 68.2.2. Launched Thunderbird and couldn't open encrypted e-mails. Turns out all addons were disabled. Had to re-install all my addons: CardBook, Enigmail, Lightning and Mail Merge.
Wondering if there is anything we can do so that Thunderbird updating also brings the updated addons.
This may not be your issue, but there are problems with add-ons for Thunderbird 68. (I am not sure from which version you are updating, for example.) From the release notes, one unresolved issue is:
When upgrading from Thunderbird version 60 to version 68, add-ons are not automatically updated during the upgrade process. They will however be updated during the add-on update check. It is of course possible to reinstall combatible add-on via the Add-ons Manager or via addons.thunderbird.net.
I use Thunderbird from Mozilla and I had re-install my add-ons when I made that transition.
Sorry, no: Thunderbird disabling plugins on upgrade is a design choice of the application, tied to how they manage plugins. The way to change that is essentially to switch to a different application.