Check setting to make sure you are actually seeing all your folders. 'Menu icon' > 'Folders' > 'All'

You do not mention any information about those 'missing' folders. Are they Pop, Imap, Local Folders folders?

If imap folders then see if you need to subscribe to see them. Right click on imap mail account in Folder Pane and select 'Subscribe'. Select folders.

I have two Thunderbird accounts. Whilst my most recent one contains Junk, Trash, Sent, etc. folders as well as Inbox, my original (and main) account shows only Inbox. I have tried the Subscribe route but the only folder I am presented with is Inbox. Are the other folders hidden or have they simply vanished with their contents?