From Archiving Messages
With Gmail, “archiving” is a built-in concept and removes the Inbox label from the conversation. After archiving, you can view the conversation by going to “All Mail” in the sidebar (which Mailspring may show as “Archive” if you have multiple accounts linked), or by viewing a label that was applied to the conversation.
Still, this is rather confusing behavior. I wonder if there’s a better way to solve this? (Maybe not.)