Extra.less will always keep your changes during upgrades.
Even if you make an edit elsewhere, let's say you add something to the template PAGE_CONTAINER for XenForo version 2.2.5. When you update to 2.2.6, if XenForo doesn't update PAGE_CONTAINER then your changes will stay and it won't be outdated.
If XenForo do change the template, your changes will still stay but the template will show as outdated. You can use the merge tool to update the template while keeping your edits.