My fault you don't understand, not yours, I'll keep trying. 🙂
Why is renaming a mailbox an option in the menu if I can't do it without making my emails disappear?
I misunderstood, thought you did it some other way, the way you did it should work, might try this.
Not certain, but this can fix myriad Mail problems...
Safe Boot from the HD, (holding Shift key down at bootup), it will try to repair your Disk Directory while the spinning radian is happening, so let it go, run Disk Utility in Applications>Utilities, then highlight your drive, click on Repair Permissions, then move these folder & file to the Desktop.
Move this Folder to the Desktop...
/Users/YourUserName/Library/Caches/Mail/
Move this file to the Desktop...
/Users/YourUserName/Library/Mail/Envelope Index
Reboot.
BTW, is this IMAP or POP?
EDIT:
Are my missing emails still in the computer somewhere?
I'd get EasyFind...
http://www.macupdate.com/info.php/id/11076
Here's a direct download link to EasyFind 4.0 which runs in 10.3.9 & up...
http://www.devon-technologies.com/files/legacy/macosx1039/EasyFind.dmg.zip
From this page,
http://www.devon-technologies.com/support/faqs.php?p=default&cat=19
Freeware applications:
* EasyFind 4.0
* PhotoStickies 5.6
* ThumbsUp 4.3
* XMenu 1.8
http://www.versiontracker.com/dyn/moreinfo/macosx/8707
Use it to search your whole drive for case insensitive & show invisibles...
.emlx
(dot ee em el ex)
Message was edited by: BDAqua