I see that there was another vector for this occurring. While previously we were not actively trying to set the addon_id to a safe value (so that XenForo wouldn't automatically delete the BB-Codes) and that was fixed in Beta 3 build 001, it turns out that XenForo had already changed the legacy_addon_id of the BB-Codes prior to the upgrade-steps running (XF\Addon\Addon::preUpgrade changes legacy addon IDs and XF\Entity\AddOn->_postSave calls XF\Addon\DataManager::updateRelatedIds), so we were still not finding the BB-Codes we wanted to save.
This additional vector will be fixed in Beta 3 build 002.
- If your upgrade was a test, you can re-run your test upgrade in build 002.
- Since you did not apply any hacks, you can also regenerate the BB-Codes in build 002 due to the Upgrade option being available again (version ID fixed). However, if some of your wiki BB-Codes had custom names, you would need to re-apply those custom names in the BB-Code manager.