Why does removing a mail account also delete the emails?

This has been a problem for at least a decade. Apple is my favorite company, but tone deaf on quite a few issues. Obviously there should just be a popup that asks if you want to keep the emails associated with the account or not.

Not sure why the "tone deaf" comment. There are, at least, four methods to retrieve "missing" messages:

1. As babowa has pointed out, your email provider may offer an option to retrieve them.
2. From a Time Machine backup.
3. From a cloned back up of your Mac's drive.
4. By using an email archiving app, like MailSteward

Regardless, I suggest that you submit your suggestion directly to Apple here: Product Feedback - Apple

> Not sure why the "tone deaf" comment.

It's because Apple's been aware for at least a decade, but never responded to it.

FWIW, I have never had an issue with removing, and then, re-adding an email account in the Apple Mail app. Regardless of which email account (Gmail, iCloud, Hotmail, etc.) I use. Note that all of my email accounts are IMAP types, and as such, the messages are stored on the appropriate email account servers.

When you add an email account in the Mail app, you are basically just creating a "pointer" to your account's email folders on those servers.

On the other hand, any messages under the "On My Mac" category, would be located on your Mac. If you delete any of these, you would have to restore them from a backup.

So do you have yours set up as a POP account? That means all emails are downloaded from the online server and are only available in your Mail app which means they will be gone if you delete it. However, depending on your ISP's settings, they may still be available if you go to your email account on their site. Most ISPs will keep those for 30 days, so you can check that first before doing anything.

What I do is before deleting any account I copy all the mailbox messages to a backup mailbox "on my Mac" Then after reinstalling the account I can move them back. I have a POP account but set the mail preferences to keep my deleted and junk for one month on server. My Yahoo server keeps my inbox and sent mail for 8-12 weeks.

Not sure why you have so many sub-boxes but you can highlite all the emails and then pick copy or send to your backup mailbox(es)