To summarize: Thunderbird does not retrieve all the messages in the inbox on the server?

Thank you for your response.

Yes, that's correct. The emails are reaching the webmail on the mail server, but they are not displayed in Thunderbird.

Even if they were being filtered as spam, I would expect them to be in the spam folder, but they are not there either.

Is it a POP account?

If it is, something may be happening that I am not familiar with. Maybe someone else can help.

You might check the account settings - Synchronization & Storage. I would enable "Keep messages in all folder for this account on this computer" and "Sychronize all messages locally regardless of age".

You might also right-click on the inbox in the folder pane, select "Properties", look in the "Syncronization" tab, and check that the folder is selected for offline use.

Were any of those settings off? Does turning them on solve the problem?

It's a POP account.

I have an update:

I found that deleting the emails stored on the mail server allowed new emails to be received in Thunderbird again.

I had set the mail server to keep emails for 14 days, in case emails weren't being delivered. It's possible that this caused the mail server to become full, preventing Thunderbird from receiving new emails.

I apologize for the complexity of the issue, but even before this incident, we were experiencing occasional problems with automatic reply emails not being delivered. I initially thought this current issue was an exacerbation of that problem, but it seems it was simply due to an overflow of emails on the mail server.

We are still investigating the "occasional automatic reply email delivery failures."

During those times, emails also failed to appear in the spam folder.