Suddenly hundreds of "sent" messages disappeared. Folder is empty, but 'properties' says there are 679 messages. So not deleted I guess. But where are they?

The only thing I changed before this happened was the 'retention' policy in my account settings with respect to retaining/deleting messages on the server. I had that set at 'never delete' while I was away for a week, but changed it to delete after 7 days on my return today. All sent messages then disappeared on the server, and I discovered later to my surprise in my computer as well. Next to the "Sent" folder in the computer there's now a small square that's filled in darkly. I don't know if the square was there before, but I'm pretty sure it wasn't dark if it was there at all. I really need those 'sent' messages - at least the most recent ones. Does anyone have any idea what's going on? Also - I could do a 'system restore', but have the feeling that won't affect my Thunderbird account at all. Is that right?

I suspect your account is an IMAP account. With IMAP all mail is managed on the server. If you delete a message in Thunderbird it is removed on the server as well, and vice versa.
So I think what happened is what's described in the article in the
'It's just doing what you told it to do' section.
More details in this article.
http://kb.mozillazine.org/Message_aging
If you want to avoid messages being deleted set the retention policy to 'never delete'.
I don't think I understand what 'a small square that's filled in darkly' is.
A system restore won't do you any good as the Thunderbird profile isn't covered.
Miscellaneous.msf won't help. Msf files are index files, and do not contain any messages.
Your best bet is to restore a backup of your profile.

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