Thunderbird Emties Spam I haven't Seen Yet

Is there a way to make Thunderbird check the server Junk folder when I open the Thunderbird Junk folder?

Not if you're using POP. You'd need to set up your account as IMAP for this. https://support.mozilla.org/kb/switch-pop-imap-account

Sorry, I guess I should have mentioned it is set up as IMAP, is there a setting I have to change?

Sincere inquiry: How do you know that messages that you never see are being deleted?

Is the folder on the server also called “Junk”?

When I click Empty Junk, to remove what I see, they show for a quick second and then they are gone, and yes, I'm sure they are different emails.

Yes, the folder on the server is also Junk

Opening the junk folder should tell Thunderbird to sync the folder with the server.

if you select the folder before emptying, my only guess is that you are not giving Thunderbird enough time to sync with the server. Do you have the status bar at the bottom of the screen enabled? You can monitor it for sync progress and postpone emptying until sync is finished.

In folder properties, enabling "When getting new messages for this account, always check this folder" may help some, but then you'll still want to get new messages or select the junk folder before emptying.

I wonder if selecting all messages in the folder and deleting them (instead of using the "empty junk folder" command) might avoid unintended deletion of messages that you are not seeing yet.

I am incredibly confused now, on my desktop Thunderbird, I've been clicking in and out of the Inbox and Junk folders and in the status bar it's doing exactly what I was asking about, and the email I thought was deleted by this issue yesterday, I saw it happen last night and I got a reply this morning that included an email from yesterday that I never saw and assumed it was the one that flashed by last night, just showed up in my Junk folder, put there by my ISP, I think, because it's not marked as junk in Thunderbird. So I'm not sure what is really going on. Is there a way to delete this thread until I find out if I have an actual problem or not? Thanks everyone for your help

As someone who doesn’t know exactly what the app is doing at a technical level, I would just say: “Odd things may seem to happen when emptying a folder during a sync process”. Then I would make sure that sync is done before emptying, and see if any more odd things happen. I do not expect them to.