Can't open attachments of archived e-mails

What does "the attachments cannot be read or opened" mean?

Without much more information, it will be difficult to help.

How many computers are involved? What version(s) of Mail do you use?

How do you archive all mail into their relevant job folders? Do you use "save as" from within Mail or some other method? If the former, what format do you choose? If the latter, please provide a step-by-step description of the process.

Do you import old emails into Mail to work with them? If so, do you do this from within Mail using the Import Mailbox menu item, or by some other method? If the latter, how do you open them?

When opened, do you see anything in the messages about attachments being removed manually? If not, what do you see?

I don't know how .Mac's Backup works, but it seems to me that you're making some wrong assumptions here. For IMAP-type accounts, messages are stored on the server. You cannot make a backup of whatever is stored locally on your disk and expect to be able to use that as an archive of what is on the server.

For you to be able to do that in Mail 2.x, Preferences > Accounts > Advanced > Keep copies of messages for offline viewing should be set to All messages and their attachments. It looks like you have it set to All messages, but omit attachments, which obviously won't work for your purposes.

If Keep copies of messages for offline viewing is set to All messages and their attachments, then Mail 2.x stores a local copy of the messages on the server using the exact same format it uses to store messages in local mailboxes, except the suffix of the mailbox folder in the filesystem is .imapmbox instead of .mbox.

You cannot import *.imapmbox mailboxes directly into Mail because when you do File > Import Mailboxes, Mail looks for *.mbox folders and ignores *.imapmbox ones, but you can easily overcome this limitation by just changing the suffix to .mbox. Note, however, that this won't work in your case either because your *.imapmbox folders don't contain full *.emlx files.

Note also that using the above procedure means relying on an implementation detail of Mail 2.x. It wouldn't work in Mail 1.x, for example, no matter what the settings.

The real issue here is that it just doesn't make sense to try to archive mailboxes that are stored on the server making backups of local data. The right way of archiving those messages would be moving them to custom "On My Mac" mailboxes in Mail.

If I understand you correctly, you are double-clicking on ".emlxpart" type files in some folder that is not in the ~/Library/Mail/ folder of the 'archive' machine, right?

As you have discovered, this doesn't work. "emlxpart" files contain attachments, but no metadata to associate them with anything, & there is no app assigned to open them directly. When removed from their original ~/Library/Mail/ folder location, there is no way Mail can know what to do with them, since there is no Envelop Index or other database file to relate them to a 'parent' message. (IOW, they are not self-contained files.) The same goes for ".partial.emlx" files -- Mail doesn't have a way to associate them with the emlxpart outside of their normal place in the database.

I believe these 'partials' are resolved into normal .emlx files eventually by Mail, since I do not see them persist over days, but I'm not sure of the exact mechanism involved. (Rebuilding the mailbox may force this, but you should verify that for yourself.)

Anyway, the point is that you can't work directly with these parts reliably after removing them from the ~/Library/Mail/ folder from which they came. You will have to import them into Mail to do that, & you will have to import the entire mailbox. The import process allows you to choose any "*.mbox" folder in your restored folder -- you do not have to import them all.

This means that if you first create a dedicated mailbox for the job in Mail & move or copy all related messages to it, you can do what you want, since the imported mailbox will be a 'child' of a mailbox named "Import" -- its contents will not be mixed with any other mailbox's.

You should be able to set up your .Mac account as either POP or IMAP in any mail client.

Does Entourage work with .Mac?

It depends on what you mean by that. Are you talking about retrieving messages from .Mac accounts with Entourage, syncing accounts through .Mac, backing up Entourage data to .Mac account storage space, or what?

From what you said in your initial post, your primary requirement seems to be archiving messages & attachments by job. This could be done with Mail, Entourage, or some other email client in a variety of ways, the most flexible of which would involve exporting these items to folders or a database instead of leaving them in any app's "native" email format. Any app with good Applescript support should work as the basis of an automated or semiautomated solution of this type, & offer some advantages (notes, cross-references, etc.) that a simple backup solution would not.

Whatever approach you decide to take, whether you decide to do it "in house" or with outside help, I suggest you first take the time to clearly define your goals in detail, then test any potential implementation thoroughly before you commit to it.