Are the mbox files still inside the Mail\Local Folders folder inside your profile folder?

Thanks for replying Stans. Honestly, I'm not sure where I would find the profile folder to check. Do I access via the C drive or is it the 'local folders' bit in Thunderbird? If the latter, there's nothing at all when I click on 'Local folders'.

See Profiles - Where Thunderbird stores your messages and other user data

Thunderbird stores messages in mbox files. They are located inside the ImapMail and Mail subfolders inside your profile folder. ImapMail is used for IMAP accounts, while Mail is used for POP accounts and the special Local Folders account. The mbox files have no file extensions. Each folder in Thunderbird has a corresponding mbox file; for example, the Inbox folder has a corresponding mbox file called Inbox. The mbox files are usually large in size, because they contain downloaded messages. They can grow to multiple GBs in size.

Phew, crisis averted. It took a bit of head scratching, and I can't definitively say I've managed to reset everything, but I've changed the profile paths and all my old emails are back. Thanks a bunch, what a relief!