Verify/repair the startup disk (not just permissions), as described in the following article:
The Repair functions of Disk Utility: what's it all about?
After having fixed
all the filesystem issues, if any, and ensuring that there’s enough space available on the startup disk (a few GB, plus the space needed to make a copy of
Inbox), try this:
1. Quit Mail if it’s running.
2. Assuming this is a POP account, in the Finder go to
~/Library/Mail/POP-username@mailserver/.
3. Locate
INBOX.mbox and move it to the Desktop.
4. Open Mail. A new empty
INBOX.mbox will automatically be created within the account folder, and this will allow you to continue using Mail normally while trying to solve the problem.
As you appear to have already found out, although
INBOX.mbox looks like a file, it’s actually a special kind of folder (a package) that contains several files. You may ctrl-click on an
.mbox and choose
Show Package Contents from the contextual menu to see the files it contains. Of these files,
mbox is the most important and is where all your messages are stored. In your case, that file is very small compared with the index (0.4 MB vs. 24.7 MB), which doesn’t sound very promising.
For completeness, let me say that an
Incoming_Mail file might also be present in the mailbox, in which case it might contain messages that Mail couldn’t transfer to
mbox.
Incoming_Mail is also a standard mbox file like
mbox proper, just named differently.
5. In Mail, do
File > Import Mailboxes and follow the instructions to import the
INBOX.mbox that’s on the Desktop. I’m not sure what the import options available in Mail 1.x are, but you should choose
Other / Standard mbox or something like that, so that Mail looks at the
mbox file only (and
Incoming_Mail, if present) and ignores the other files in the package.
If Mail doesn’t let you select
INBOX.mbox in step 5 because it’s a package instead of a plain folder, rename
INBOX.mbox to just
INBOX (i.e. remove the
.mbox suffix) so that it becomes a normal folder, and try again. You cannot do this directly in the Finder because removing a suffix by normal means causes the Finder to
hide the suffix instead of renaming the file. To remove the suffix from the name, you must do
File > Get Info (⌘I) on the file and change the name there.
Do with the imported mail whatever you wish. You may move the messages anywhere you want and get rid of the imported mailboxes afterwards.
If all is well and you don’t miss anything, the files on the Desktop can be deleted, although you may want to keep them for a while, just in case.
Note: For those not familiarized with the ~/ notation, it refers to the user’s home folder. That is, ~/Library is the Library folder within the user’s home folder, i.e. /Users/username/Library.