More info: Inbox and inbox.msf are tiny, apparently just including the most recent emails from today. I see that inbox.mozmsgs has mail in it. From the dates and info I can read, I know this is email that was in my email box. When I search for messages I know were in my inbox, they appear in the search results, but when I click to read them, they are not there.

Sometimes the index of a mail folder (.msf) will get corrupted. If you right click on the name of the folder and select Properties, a 'Folder Properties' window will open. Select 'Repair Folder'. Try that on inbox.mozmsgs

Thanks. Did try that and it seemed to "repair" only the tiny inbox folder that contains mail from the past two days, since this happened. I repaired other folders as well, which were unaffected by the original problem and it made no difference.

Since this happened after a crash, there is some possibility you now have more than one TB profile. Look in your (home).thunderbird directory to see if you have more than one ********.default profile. If so, the mail before the crash could be in the profile you are not currently using.

See https://support.mozilla.org/en-US/kb/profiles-tb and

https://support.mozilla.org/en-US/kb/using-multiple-profiles

If you are still having problems, please look at the following items and respond with the information.

   1) What operating system do you use (Win8, MAC, Linux, etc)?
   
   2) Are you using IMAP or POP?

   3) If your mail server has a browser interface (web mail access such as mail.google.com), do the messages show up there?
       
   4) Right click on the folder in question and select Properties.
       a) Number of messages?
       b) Size on disk?
       
   5) Left click on the account name; View settings for this account; highlight Server settings;
       What choices are marked under "When I delete a message"?
   
   6) What, if any, antivirus program do you have installed?

Just one profile appears, so that doesn't appear to be the problem.

On your questions:

1) What operating system do you use: Windows 7
  
  2) Are you using IMAP or POP? POP
  3) If your mail server has a browser interface do the messages show up there?  No, they were downloaded locally.  
      
  4) Right click on the folder in question and select Properties.
      a) Number of messages? 104
      b) Size on disk? 47.7 MB
       But this is probably not the question you want to know, since this is the size of the folder and the mail I've received only after the crash and the disappearance of the email.  At the time the folder failed, I would estimate it had around 1500 messages and probably close to 1GB in size.  
      
  5) Left click on the account name; View settings for this account; highlight Server settings;  What choices are marked under "When I delete a message"?  

There is no "when I delete a message" option under server server settings for this account. "Check for new messages at start up." "Check for new messages every 10 minutes," and "Automatically download new messages" are all checked under server settings. Fetch headers only and Leave messages on server are not. From a quick search online I see that this is not a POP option.

  6) What, if any, antivirus program do you have installed? McAfee Security Scan Plus

Thanks. Still hoping to recover the lost messages.

If you have time and inclination, please look at the following. Do this procedure on both Inbox and Inbox.mozmsgs.

Using your file explorer, go to your inbox file, right click on it, and open it with Notepad. The format is a little difficult to read, but each email starts with "From - <the date sent>" You can use the 'find' function to look for the next message: search for "From - ". The next line after "From" starts with "X-Mozilla-Status: <a number>" There are two things I want you to look for:

   a) do you see any (or all) of your missing emails?
   b) what is the number after X-Mozilla-Status (at least on a few of the missing ones)?