After customizing my Mail Toolbox the Junk mailbox disappeared and Trash mailbox stopped showing trashed messages from that point on

Hello nes76,

Thanks for visiting Apple Support Communities. If we understand correctly, after customizing the Mail toolbar you no longer see the Junk folder and Trash no longer appears in the Trash. If that's correct, start with checking the Mailbox Behaviors to see what's set for Trash. Here's how: Change Mailbox Behaviors preferences in Mail on Mac

Regarding the Junk folder, is it missing from the toolbar or the sidebar list of folders? If the toolbar, do you see it to add back when you customize again: Customize toolbars on Mac

If it's missing from the sidebar, hover your cursor over favorites and choose the +. From the list choose the Junk folder: Use favorite mailboxes in Mail on Mac

Let us know how it goes.

Take care.