Erasure of junk mail erases all mail in inbox.

Hi there japper1,

Welcome to Apple Support Communities. We understand you have an interesting issue with Mail and deleting Junk messages. We'd like to work with you to figure out what's going on and have some questions.

1. Which mail provider is your email account with?
2. Do you have more than one email account configured?
3. Do you use any other Apple devices with the same mail account configured?
4. If you just delete a single Junk mail message, does the same thing occur?

We'd also like to have you test for this issue in another user profile. This will help narrow down the issue to either a system-wide, or user profile specific concern. You will need to create a test user profile with admin privileges, log in to it, then configure Mail for your account and test.

Set up users, guests, and groups on Mac

We look forward to hearing back from you.

Take care.

Hi japper1,

With it working properly in the second account, let's see if it also occurs in safe mode on your Mac. This will let us know if any 3rd party software is potentially interfering with your Mail app and causing this to happen: Start up your Mac in safe mode

"Before you begin

To start up your Mac in safe mode, you need to know what type of Mac you have.

1. On your Mac, choose Apple menu  > About This Mac.
2. Look at the information in the window to determine what type of Mac you have:

• If you see an item labeled Chip, followed by the name of the chip, you have a Mac with Apple silicon.
• If you see an item labeled Processor, followed by the name of an Intel processor, you have an Intel-based Mac.

1. Use the corresponding set of instructions below to start up your Mac in safe mode.

Start up your Mac with Apple silicon in safe mode

1. On your Mac, choose Apple menu  > Shut Down.
2. Wait for your Mac to shut down completely. A Mac is completely shut down when the screen is black and any lights (including in the Touch Bar) are off.
3. Press and hold the power button on your Mac until “Loading startup options” appears.
4. Select a volume.
5. Press and hold the Shift key, then click Continue in Safe Mode.
6. The computer restarts automatically. When the login window appears, you should see “Safe Boot” in the menu bar.

Start up your Intel-based Mac in safe mode

1. Turn on or restart your Mac, then immediately press and hold the Shift key until you see the login window.
2. Log in to your Mac.
3. You might be asked to log in again.
4. On either the first or second login window, you should see “Safe Boot” in the menu bar.

Verify your Mac started up in safe mode

If you’re unsure whether your Mac started up in safe mode, you can use the System Information app to check the mode.

1. On your Mac, press and hold the Option key, then choose Apple menu  > System Information.
2. In the System Information app, select Software in the sidebar.
3. In the System Software Overview, look at the value listed next to the item labeled Boot Mode.

• Safe: The Mac is using safe mode.
• Normal: The Mac is not using safe mode.

"

If the issue does not occur in safe mode, then you'll need to try removing all of your login items on your Mac, and adding them back one at a time to see which software is interfering with Mail: Remove login items to resolve startup problems on your Mac

We hope this helps.

Cheers.

Hello japper1,

Welcome back to Apple Support Communities!

You're very welcome! It sounds like these steps might have resolved the issue.

Please reach back out again in the future if we can further assist you. We appreciate you working with us.

Cheers!

Thanks for the additional details, japper1,

We look forward to hearing how the test goes. This will help us rule out possible underlying causes.

Thank you.