Question about Sent Mail folder contents

Hi Everyone.
this question requires a fair amount of background -- I tried my usually very helpful users' group and didn't get any responses. Here's the story:
I upgraded my macbook pro to Leopard partly because I thought Time Machine would make me backup more regularly (it has). I have a few sporadic backups from prior to the upgrade, and then I backed up right before I upgraded. I had a disk error during my first attempt at an archive & install, found that the disk was wiped, thanked my lucky stars I backed up beforehand, ran disk utility on the disk, and then did an erase & install instead.
After the upgrade, I used the migration assistant to restore my user account from my backup. At some point after the fact, I noticed that my sent mail mailbox in mail.app for my primary email account was missing all my emails except for the period from 3/30/05 to 4/15/05 and from 1/07 to 4/07.
I thought I was hosed, but today I found I had another backup on a second disk, and that one has 10,614 emails in the sent mail folder (to be precise Sent Message (account name).mbox/Messages/). After importing, I have all of those sent emails restored in a folder in mail.app.
However, during this process, I went and checked my Sent Messages mailbox in my current Library folder for this user account. In that folder (Library/Mail/Mailboxes/Sent Messages (this account).mbox), all of the files (content_index, Incoming_Mail, IncomingTable_ofContents, mbox, and tableofcontents) show an incorrect(?) created / modified / Last opened date of 5/26/05. The Info.plist file has the correct dates, and the Messages folder does, too. Those same files are in the Sent Messages folder on both of my backups, and have the same date (5/26/05) listed.
I actually pulled all of the files listed above with the weird dates and removed them from the Sent Messages.mbox folder. That doesn't seem to matter to mail -- everything still seems to be working just fine.
So, my question is, are those files crucial, or are they cruft from multiple generations of OS updates and mail.app updates that are no longer needed? It seems like no new versions were automatically generated when I removed the old ones, and mail doesn't seem to be broken.
I've been using mail.app at least since 2004 and the emails in the sent mail folder trace back to a Pbook G4 that started with OS X 10.1 (maybe even 10.0 -- my memory isn't as good as it used to be) and was upgraded with each major release, then I migrated to the current MacBook Pro and upgraded it from Tiger to Leopard. So I've probably used the migration assistant (or archive & install) to help me move files (or did it manually) through one laptop changed and four OS upgrades.
Any ideas about this Sent Messages question or in general about how I might clean up my Mail folder are appreciated.
Thanks!

I have both POP and IMAP email accounts.
The IMAP is easy. Until you delete it is visible on both phone and computer. Once you delete it is gone from both, although with providers like Google, you can still un-delete it. Google, among others, provides free IMAP email.
For POP, there is a setting in Entourage preferences, (maybe in mail.app, too) that will let you decide to automatically delete the mail from the server, manually delete the mail from the server, or automatically delete after a period of time. I set my pop account to automatically delete from the server after one month. You set up the iPhone the same way - to leave it on the server. This way, a message will download to both your computer and to the iPhone. If you are working at your computer, you can still manually delete the message from the server so that it does not go to your iPhone, since you have already handled it. But even if you never delete from the server, it will automatically delete in a month so that you do not go over your email limit (if any) for your ISP.
Also, with my POP account, I set up the phone to automatically send a copy to me of all outgoing messages. This way my computer has a copy of everything I send from the phone.

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