It seems if you have too many files in your Mail.app message could disappear (visually)

Apple has calls it "Overstuffed mailbox is unexpectedly empty"

Reason:
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How large does the mailbox have to be for this to happen? With Mac OS X 10.4 or later, 2.0 GB or larger. With Mac OS X 10.
3 through 10.3.9, there's not a specific size where this will always occur--the mailbox could be anywhere from a few hundr
ed megabytes (MB) to over a gigabyte (GB) large. However, the bigger your mailbox (or combination of mailboxes) is, the mo
re likely it is this could occur.
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Apple suggest these steps:

* Update to the latest version of Mac OS X 10.3 or 10.4. Even if this works, check out "How can I prevent it from happ
ening again?" below.
* From the Mailbox menu, choose Rebuild.
* Quit Mail and open it again. If Mail had been open a while, this might help. Even if this works, check out "How can
I prevent it from happening again?" below.
* If you use more than one account, for example "Account 1" and "Account 2", instead of clicking on the "In" mailbox,
click on either "Account 1" or "Account 2" that appear beneath "In" (as well as beneath Sent and Trash, for example). That
way you'll only see messages related to that specific account. If your two account mailboxes are big individually, but no
t big enough to cause this issue, when viewed together (by just clicking "In" for example), the issue may occur.

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