This is not a reply, but question owner adding more information.

1) I've read many forums with similar problems (none exactly the same), but I am not a IT guy, so I don't understand half the answers. However, I did check Profile, but there is nothing there except the Inbox file itself. Hence none of the forum answers I have seen seem to answer my problem.

2) I have several accounts, most of which running in IMAP using their own account inboxes. These seem to be working fine.

3) However I have several accounts using POP, where I wanted to amalgamate all emails into one subfolder structure, rather than having the same or similar subfolder structure account by account. So I set these to save into Local folder as subfolders of the inbox. The subfolder structure was linked with filters which automatically moved incoming emails into the right folder. Up to now this was working fine.

4) What suddenly disappeared a few days ago is the whole subfolder structure and all the emails saved in each of the subfolders. Also gone were all emails in the inbox itself (those odd ones for which I didn't have a folder or filter).

5) Essentially everything in inbox is gone. But all new emails since the day it happened are being stored in the inbox (the filters don't work any more because the folders are gone) as before.

Luckily nothing is ultimately lost, since I'd set the the accounts to save emails on server for 150 days (now changed to 250) - this was an experimental move from MS Outlook in May 2014 - if I cannot get Thunderbird to work, I'll have to revert back to Outlook (i.e. I can still re-download all my emails there, currently disabled).

I am disappointed this has happened, I'd prefer to move away from Outlook, but ......... .

This may be related. I have Windows 8.1 I have 2 accounts, a local account & an administator account. (Windows accounts not email accounts)

Both have thunderbird with various imap accounts. I pointed the Thunderbird in my local account to the mail folders in the administrator account. In this way , both instances of Thunderbird point to the same mail folders and more particularly to the same Local folders. All worked fine for months. 3 days ago the Local Folders subfolders dissappered. They are still there and searchable, just not displayed. All I did to fix it was open Thunderbird as administrator and the folders were there. When I closed TB and opened it as normal the folders were back to normal.

I think the Local folders subfolders were changed by windows to either read only or hidden or system and opening as administator fixed it.

Try running Thunderbird as administrator (right click ans select "Run as administrator" ( or for windows 8 right click the icon on the taskbar, then right click again Mozilla Thunderbird then select "Run as Administrator" ))

You will need your administator password if you have one set.

Windows 8.1 does some really stupid things and seems to do them randomly. Its probably Microsoft version of "We are trying to protect you...which probably really translates as we are going to randomly break other software so you will have to use ours"

Whilst your circumstances of where the files are locatd are different it may be worth a try anyway.