What type of account is this (POP, IMAP)?

If IMAP, right-click on the account in the folder pane and choose Subscribe. Do the missing folders appear there checked or unchecked. Check the folders you want to appear in Thunderbird that are not already checked, then click Subscribe, then OK.

Take a look at the view options in the following article, in case you're simply getting confused by the different ways in which accounts and folders may appear in the folder pane (All Folders / Unified Folders): https://support.mozilla.org/kb/switching-folder-pane-view

Sorry for the delay. I have been trying to problem solve. I found the missing folders. I think this is not IMAP. The server settings are pop-server.wi.rr.com The strange thing is I have 2 inboxes. One is wheeler@wi.rr.com and the other is just called wheeler. My mail is being oddly split between the two. Question for you all: I normally update Thunderbird by going to Thunderbird and updating from within the program. I last updated Thunderbird with a patching program. So the version is 128.7.1esr and I am on the esr update channel. What is the esr channel?

One is wheeler@wi.rr.com and the other is just called wheeler. My mail is being oddly split between the two.

This sounds like you're using Unified Folders view and have set up the account twice in Thunderbird, one using the whole email address as the username, the other using only the part to the left of the '@' as the username. To check whether this is the case, go to Account Settings and see whether the two accounts are listed there on the left.

Are both accounts active, i.e. do both inboxes receive incoming messages? Are the messages the same in both (i.e. same account) or are they different accounts? Are both accounts of the same type (POP, IMAP)?

So the version is 128.7.1esr and I am on the esr update channel. What is the esr channel?

https://support.mozilla.org/kb/thunderbird-128-nebula-faq#w_why-is-thunderbird-128-labeled-as-128-0esr-when-previous-versions-were-not-called-esr

I don't know the details. I let Thunderbird check for updates, but not install them. I manually download the version I want instead.

sorry for the delay. I am not using unified folders view. Both wheeler@wi.rr.com and wheeler are listed under account settings. Both are POP type and both are receiving mail. The messages are not being duplicated. For example, I don't receive 10 messages in wheeler@wi.rr.com and get the same 10 messages in wheeler. My incoming mail is getting split between the two inboxes. If I get 10 emails, some will go to wheeler@wi.rr.com and some will go to wheeler.

Under the link you posted, there is this question listed: "Why are my Thunderbird customizations broken in 128?" I was using version 115 and everything was working perfectly. Version 128 is COMPLETELY different than 115.

Question. Is there a way to remove the wheeler account without screening things up?

OK. You appear to have somehow set up the same account twice in Thunderbird, and it would seem you were able to do that because the mail server accepts as username both the whole email address and also only the part to the left of the '@'. Can you verify that? Also, you don't have to guess whether the account is POP or IMAP, Thunderbird shows the type of account in Account Settings > Server Settings > Server Type.

Post a screenshot of your full Account Settings > Server Settings for each. Looks like you've configured them to remove messages from the server after downloading, and hence the messages downloaded with one aren't available to the other.

Pick one of the accounts as the one to keep (I'd pick the one that uses the full email address as the username), uncheck all the options to check for mail on the other, and check on both the options to leave messages on the server for 30 days or until you delete them in Thunderbird. This should make all your mail go to one of the accounts and not the other unless you manually check for new mail on that.

okay I did what you said about unchecking the "check for new messages at startup" on the wheeler account, but left that setting checked on wheeler@wi.rr.com. Now when I start Thunderbird, it doesn't check for mail automatically on either account. I have go to file on the menu bar and select "get messages for" and then choose the wheeler account. (when I do this the messages are again split between the two accounts.) If I choose the wheeler@wi.rr.com account nothing happens.

this is a screenshot of my inbox. Notice my sub-folders under local folders/inbox. In previous versions of Thunderbird, that is where all of my mail went and I had filters separating mail into different sub-folders. It just worked perfectly. This version of Thunderbird is completely different. I wish I had a screenshot of old versus new. Question: could I uninstall this version of Thunderbird and reinstall version 115 as I actually have it on computer. Then try to update to 128 from within Thunderbird using the help/about menu? Or will Thunderbird not let me install an older version? Thanks for your help and time spent on my issue

You have a weird setup there. I need to take a closer look at that, but something you should do right now is check Leave messages on server on the wheeler account, because the way you have it configured now, that account could be deleting from the server messages you might want to be downloaded by the other account…

OK. There are a lot of things amiss there, but all of them can only be the result of things you've done yourself. They cannot be attributed to a Thunderbird update and they wouldn't be fixed by installing any particular version of Thunderbird. You may try downloading and installing a previous version of Thunderbird if you want, but don't expect that to fix anything there.

The only way a Thunderbird update might have something to do with this mess is if you have multiple profiles and Thunderbird is using the wrong profile now for some reason. The mess within the profile would still be your sole responsibility, it's only having chosen an erroneous profile that could be attributed to a Thunderbird update. So take a look at the following article to see how you may check whether you're using the right profile and try choosing another one that may also be available:

https://support.mozilla.org/kb/recover-user-data-missing-after-thunderbird-update

I'll wait until you post back with your findings, if any, before giving further instructions on how to try to fix the mess you currently have.