Nothing irrevocable or harmful happens to emails you choose to archive. They are moved out of your Inbox and held safely in the Archive mailbox until you need them.
Moving an Email to the Archive Mailbox
Select a message in Mail and press the Archive button at the top of the Mail screen or select Message > Archive from the Mail menu bar to move the message or thread to the account’s Archive mailbox, where you can quickly find it later for other actions. It is not deleted. If you prefer using a keyboard shortcut, Control+Command+A moves a selected email to the Archive mailbox. Laptops with a Touch Bar display the Archive mailbox icon when you select a message. Tap the Archive icon in the Touch Bar to send the message to the Archive mailbox. Mail automatically generates a mailbox called Archive for each email account. If no archiving mailbox exists for the account, Mail creates a new mailbox called Archive automatically the first time you archive a message in one of your accounts.
Where to Find the Archive Mailbox
If the Mailboxes sidebar isn’t already open in Mail, click Mailboxes under the Get Mail button at the top of the Mail screen to open the Mail sidebar. The Archive mailbox is in the Mailboxes section of the sidebar. If you only have one email account, all your archived messages appear in this mailbox. If you have several email accounts, expanding the Archive mailbox reveals a separate Archive subfolder for each account you use. Click the Archive mailbox to see any email you have archived in the past. The messages remain in the Archive mailbox until you move them or delete them.