Where did the check boxes above email go?

Since you mentioned that you already explored the settings and managed to restore one of the missing checkboxes, could you please clarify which one is still missing? Is it the checkbox beside individual emails or the checkbox at the top of the message list that allows you to select all messages? To restore the selection checkboxes, open Outlook.com > Settings (gear icon) > Mail > Message list, then scroll down to Layout > How do you want messages to appear in the message list? and select Checkboxes instead of Sender images or Name only. This should display checkboxes beside individual messages and, in supported layouts, the checkbox near the folder name for selecting multiple emails.

Alternatively, if you have Sender images enabled and prefer keeping the profile pictures visible, move your mouse pointer over the sender's profile picture or initials beside an email. The picture should temporarily change into a checkbox that you can select. Once you select a message, Outlook should enter selection mode, allowing you to select additional messages using their checkboxes. This is another way to select multiple emails without permanently changing your message list layout.