I read your post to say that several months ago you moved a large number of messages out of the "Mail in" folder but the message count didn't change because of an index problem.  The index problem is also why messages wouldn't open.  Rebuilding the index corrected the message count to 92.  The rest of the messages should be where you moved them.

You also mention a folder that has grown from a few hundred to several thousand.  To help you troubleshoot consider that the only way messages get moved to folders are:

1.  From the New mail folder to the configured default mail folder if read mail is not allowed to stay in the New mail folder

2. Manually

3.  With filters, either filtering rules or auto-filters

A baffling problem: I have a 'Mail in' folder which held some 4000 messages. I've sorted some old mail a few months back moving large batches of e-mails out of this folder so that it wouldn't be too complex. Ever since I'm having problems with my folders, one has grown from a few hundred to several thousand emails after a problem. The 'Mail in' folder was showing over 4000 messages but many of them wouldn't open. I then checked it, the prompt suggested a re-index and now I only have 92 messages in that folder. Where did the rest go??

Any suggestions on how to proceed are very welcome!