We are phasing out Zendesk. Please see Discourse instead: https://community.getmailspring.com/t/cannot-label-or-archive-some-messages/287
If you're using unified inbox or switching between two different email accounts, you may notice that the label and archive features disappear from the toolbar for certain conversations.
Mailspring only allows you to apply labels to Gmail conversations, and only allows you to Archive messages in accounts that have an Archive folder. In unified inbox, Gmail conversations may appear side-by-side with conversations from non-Gmail accounts (like Office 365), so labels will only be present on some items.