I am using Evolution 2.24.5 on Fedora 10.  I don't think the distro is
important here.  I am seeing this same issue.  I typically move my email
to an archive folder when I think I am done with it, so I rarely have
more than 100 emails in my inbox.  However, some of them can be a few
weeks old.

This is germane because I will have random incidents where some messages
will disappear from Evolution.  It's not all messages or even all
messages before X date.  It's not all messages received after some point
in time.  Sometimes it will be messages a few minutes old.  Sometimes
messages from a few days ago.  But I will generally still retain some
messages both newer and older than the disappearing messages.  I have
noticed that threads tend to disappear as an atomic unit.  The
disappearances tend to happen after restarting Evolution which I mainly
have to do on reboot, but I believe some occurrences happened when
simply changing folders.

The messages are not really gone.  I can log into Webmail (Is there any
other user interface that screams, "We hate users!" quite so
vociferously?) and still get to them.  Sometimes moving them to another
folder and moving them back to the inbox will cause them to reappear in
Evolution, sometimes not.

When messages disappear like this, the unread count for the inbox goes
haywire.  Sometimes it will reflect the new messages I can see in
Evolution.  Sometimes it will reflect the new count on the server.
Sometimes it will reflect a random number in between.

As reported by others, I only see this with Exchange.  I never have
problems with my local archive folder.

Seeing the advice above about removing folders.db, I tried to see if I could 
narrow it down.  I did this:
- Shutdown Evolution
- Made a backup of folders.db
- sqlite3 folders.db
- delete from 'personal/Inbox';
- Started Evolution

This worked for me.  Just clearing that one table forced a server resync
for the inbox folder.  It definitely seems like a corruption issue.  If
it helps, the missing messages were no longer in the personal/Inbox
table at all.  It wasn't a matter of having corrupt data in the table.
I had 39 messages in my table before I purged and 111 after I resynced.

-- 
missing message in the inbox folder
https://bugs.launchpad.net/bugs/160142
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