mrsfuss,
Here are a few things to mix & match to see if they can get you up and running again. Sorry about the length - 'Brevity' is obviously not my middle name...
1) Junk Folder: If you've suddenly acquired a folder/mailbox called Junk, and new mail is running off to hide in there, that's because Mail's built-in spam filtering feature has been switched on, even if you weren't using it before. I found the same thing happened to me when I first cleared out my accounts list and relaunched Mail to rebuild it, so presumably it's a default setting when Mail is reinitialised.
This can be turned off in Preferences under the main Mail menu, third tab in the window that pops up. You can then move or delete any mail that's already sitting in Junk, and delete the mailbox. I forget if Mail allows you to delete the mailbox within the application itself; if not, you can get rid of it via brute force over in the Mail directory of your user library.
(As a side note, personally I've used SpamSieve for years for spam filtering, which does a fantastic job learning as it goes via Bayesian filtering. It's easy to correct as you go along, including the ability to review and manually modify the specific rules it has created based on sender, key words, etc. I heartily recommend it.)
2) Archive Folders: Not sure how these would have appeared out of the blue. An Archive mailbox is created when you select one or more emails and choose the Archive option under the Message menu (also available by right-clicking on them). I'm not sure what service this provides v. moving things around yourself to get them out of your inbox (they're still indexed for searches, etc.). Perhaps it's just offered as an easy solution for basic users.
I gather Mail thinks it owns the right to create and control any folder/mailbox called 'Archive', so things can apparently get messy if you create your own mailbox with the same name.
Moiving forward, you should be able to move all these emails to other folders easily (or delete them). In my case, Mail wouldn't allow me to delete the empty mailbox, however. If you really want it to disappear, you will have to delete it from the Mailboxes directory, and edit it out of accounts.plist. Perhaps for now it's best to leave it alone and see if it becomes useful in the future.
3) Corrupted Mailboxes: Often if Mail isn't displaying messages correctly within a mailbox, or showing incorrect new message counts, etc., this can be corrected by selecting the mailbox and choosing the Rebuild option under the Mailbox menu. Alas, I've found this less reliable under this first release of Mavericks. If this doesn't work, here is what I think is a handy solution for hunting down all your missing/corrupted emails following the Mavericks upgrade...
4) REIMPORTING LIVE MAILBOXES TO REBUILD & REARRANGE: Using the Import option under the File menu, you can go off to your user Mail library and reimport any mailbox as a new mailbox, without corrupting or changing the source in any way! This means you can even reimport live mailboxes! Chose the 'Apple Mail' option in the dialog box that appears, and go off hunting down any and all MBOX files in your user mail directory (main directory, V2 subdirectory, nested personal folders, etc.). Navigation and selection is easiest if you have first added your user library to Finder Favourites.
When you do this, Mail will create an Import folder, and shove a shiny new copy of the mailbox under it, with the same name. Again, because it puts it under this subdirectory, the original mailbox is not touched. If you select multiple mailboxes on a single run, they will each appear separately. If you prefer to do this one mailbox at a time, Mail just creates copies of the Import folder: Import-2, Import-3, etc. Once you've pulled all your old stuff in, you can tidy up and move things around to the correct folders. Sometimes it's just enough to verify the total email count v. your old folder to give you peace of mind.
Note: if you have nested folders/mailboxes anywhere, the Import utility will only grab email from the top level. You then need to navigate down and select each nested mailbox separately for its own import.
5) Duplicates?: If the end result of all of this is lots of duplicate emails, more then you feel up to dealing with manually, there are scripts out there that can do the job for you. One I have used in the past on a friend's Mac is:
http://c-command.com/scripts/eaglefiler/remove-duplicate-messages
It flags duplicates and moves them into a separate folder. Can't confirm if this works on Mavericks, but if loads and is accessible, the script is probably safe to run.
6) New Mail Still Missing?: If after all of this you think some of your recent inbound email is still MIA, the index in Mail that matches downloaded mail to your mail host is MessageUidsAlreadyDownloaded, which can be found hanging around and smoking cigarettes with Accounts.plist in the same MailData directory. Delete/move/rename this, and Mail will think every email on the server is new and download it again. (Also, if you ever have a problem with mail on your server being dowloaded over and over again, this is your likely culprit; the above-mentioned friend somehow ended up with multiple copies of the same file and it was making Mail (and him) go mental.
7) A Final Caveat: [Readers who are still awake let out a long sigh, followed by reluctant applause...] I've written all of this from my personal perspective of using mostly multiple POP accounts, and only one IMAP account. It's my understanding that IMAP email gets copied locally when you move it to separate folders outside of the account, so it still applies. I hope someone will correct me if I'm wrong. If youre troubles lie within mail folders created directly under your IMAP account so they sync with your iPhone, etc., I really may not have a clue what I'm talking about.
I don't use GMail a lot, but I also gather the cold war between Apple and Google may be hotting up, and Gmail users are having an especially hard time with Mavericks. It doesn't seem clear yet whether this is due to bugs, a standards war, or simple bloodymindedness.
I hope at least some of this is helpful to you or othersl. 'Likes' are always welcome ('Points mean Prizes!'). If I'm hopelessly deluded on anything I've written, please someone correct me.
Have 'fun'!
