Nicky,
I only was asking if those started in an older version of OSX were on any Mac that was upgraded to 10.4 or 10.5, or the Mail folder was migrated to a new Mac with the new OSX?
Quit Mail, and in the Finder open Home/Library/Mail. Make a Duplicate of the Mail folder, and drag the resulting copy to the Desktop another location for temporary backup.
Open the older POP account's folders, and then open the INBOX.mbox folder to start with. Remove all files except the Info.plist file and the Messages folder (with its message content). Any other files are leftovers from earlier versions of Mail, and while not actually used, can be problematic to proper indexing. Do the same for the Sent Messages.mbox folder, and either delete the Junk.mbox and Drafts.mbox or clean them up similarly. The Deleted Messages.mbox can be dealt with either to delete the folder, or similar cleanup.
Do this for each POP folder, although those less than a year old will likely not have any leftover files.
Next, in the Mail folder, open the Mailboxes folder. There open each xxxx.mbox folder and look for the same leftover files to remove.
Finally, again remove the Envelope Index and then relaunch Mail again. It should announce it is ready to Import your mailboxes -- allow this to continue, and it will reindex every mailbox.
For my authority that these are no longer needed, leftover files see:
http://support.apple.com/kb/TA23076
When the new form of mailboxes came into use, conversions of older mailboxes was often incomplete. There is a whole list of comparisons, and things to do to have a more complete conversion, but since you have been using the new versions of Mail for quite some time, I assume you are not needing to try to find any messages that failed to be converted from when you used 10.2 or 10.3, so I have not gone into that. However, the duplicate copy I had you make could be used for that, later.
Ernie
