Emails in local mailboxes disappearing

I have a POP account and I'm accessing it only from one machine, my G5 dual 2GHz with 8GB RAM. Since I switched over from Eudora over the weekend, Mail.app has caused no end of headaches for me.
Occasionally, emails stored in various "On My Mac" local mailboxes have seen fit to just vanish, leaving what looks like a blank mailbox. Rebuilding the mailbox doesn't work. On the occasions that the emails do show up as a list, when I click on any individual email, it displays the infamous "The message from <Name> <[email protected]> concerning <Subject> has not been downloaded from the server. You need to take this account online in order to download it." message (which shouldn't be happening since the emails are already stored locally on my hard drive--this is a POP account after all and nobody has access to it but me and I'm only using one machine to access it). I have to re-import the emails using Mail.app's built-in menu option to do so. I cannot use the "remove the Envelope Index" trick because, in total, I have in excess of 560,000 emails in over 460 mailboxes that I need access to when searching for emails on a certain topic and having Mail.app reindex everything takes something close to 5 hours. I cannot be down for 5 hours. I have already run "Repair Permissions" using Disk Utility and have gotten a clean bill of health.
Is there anything I can do to make sure that my locally-stored emails just display their contents and not give me the dreaded " The message from <Name> <[email protected]> concerning <Subject> has not been downloaded from the server. You need to take this account online in order to download it." message or just display blank mailbox(es) and not have to rebuild the damned thing(s) all the time? Why is Mail.app so fragile anyway? I've used Eudora for decades in POP mode and have never experienced the problems that Mail.app has given me in a mere weekend.
PowerMac G5 dual 2GHz & MacBook Pro Core Duo Mac OS X (10.4.9)

The recommended mailbox size limit for Tiger Mail is
2GB. Do any of 460 mailboxes approach or exceed this
limit?
I thought this artificial limit was removed after Panther? You're saying that it still exists? I sort my mailboxes by years so they are stored in this hierarchy:
<Topic> (contains current messages about <Topic>)
- <Topic>-200x (contains messages about <Topic> in year 200x so there could be many mailboxes at this level; when 2007 ends, I will have a <Topic>-2007 mailbox which I will move all email about this topic into, leaving the <Topic> mailbox only containing current emails for the year on that topic)
Now, this 2GB limit, is it just for the *.mbox folder or for just the Messages folder or for any hierarchy? When I do a "du -k" in some of my hierarchically filed mail, e.g., ~/Library/Mail/Mailboxes/Apple Lists, I get this:
1608 ./ACN/ACN Forums 2001.mbox/Messages
1612 ./ACN/ACN Forums 2001.mbox
11096 ./ACN/ACN Forums 2002.mbox/Messages
11100 ./ACN/ACN Forums 2002.mbox
31744 ./ACN/ACN Forums 2003.mbox/Messages
31748 ./ACN/ACN Forums 2003.mbox
65524 ./ACN/ACN Forums 2004.mbox/Messages
65528 ./ACN/ACN Forums 2004.mbox
130860 ./ACN/ACN Forums 2005.mbox/Messages
130864 ./ACN/ACN Forums 2005.mbox
175032 ./ACN/ACN Forums 2006.mbox/Messages
175036 ./ACN/ACN Forums 2006.mbox
415888 ./ACN
243280 ./ACN.mbox/Messages
243284 ./ACN.mbox
856 ./AppleScript.mbox/Messages
856 ./AppleScript.mbox
56 ./ARD.mbox/Messages
56 ./ARD.mbox
2652 ./Cocoa Dev.mbox/Messages
2652 ./Cocoa Dev.mbox
192 ./Mac Net Prog.mbox/Messages
192 ./Mac Net Prog.mbox
536 ./OpenGL.mbox/Messages
536 ./OpenGL.mbox
464 ./OSX Client.mbox/Messages
464 ./OSX Client.mbox
34624 ./OSX Svr/MacOS X Server Topics 2002.mbox/Messages
34628 ./OSX Svr/MacOS X Server Topics 2002.mbox
98904 ./OSX Svr/MacOS X Server Topics 2003.mbox/Messages
98908 ./OSX Svr/MacOS X Server Topics 2003.mbox
159824 ./OSX Svr/MacOS X Server Topics 2004.mbox/Messages
159828 ./OSX Svr/MacOS X Server Topics 2004.mbox
163916 ./OSX Svr/MacOS X Server Topics 2005.mbox/Messages
163920 ./OSX Svr/MacOS X Server Topics 2005.mbox
119972 ./OSX Svr/MacOS X Server Topics 2006.mbox/Messages
119976 ./OSX Svr/MacOS X Server Topics 2006.mbox
577260 ./OSX Svr
27828 ./OSX Svr.mbox/Messages
27832 ./OSX Svr.mbox
32 ./System Imaging.mbox/Messages
36 ./System Imaging.mbox
116 ./XSAN.mbox/Messages
116 ./XSAN.mbox
1269176 .
Which, as you can see, totals out to around 1.26GB for the ~/Library/Mail/Mailboxes/Apple Lists hierarchy and none of the individual .mbox or Messages folders exceeds 2GB. And some of the above folders have been the ones exhibiting the vanishing emails (i.e., they are there when I look at something once and then they are gone the next time I try to look again in those mailboxes). I've even experienced the disappearing mailbox phenomenon in mailbox hierarchies which, in total, do not exceed 500MB for all subfolders.
The "has not been downloaded from the server" error
message is not accurate and indicates what is called
an "overstuffed" mailbox issue which means the
mailbox has approached or exceeded the recommended
size limit or the mailbox has some corruption.
Oh crap. Sigh. I never had this issue with Eudora which has a 32767 email limit regardless of size of individual emails, attachments, etc.
Using the Finder, go to Home > Library > Mail. All
imported mailboxes are located within an Import named
folder located within the Mailboxes folder - Home >
Library > Mail > Mailboxes > Import > imported
mailboxes - which appear as folders at the Finder
level and include an .mbox extension.
Within any .mbox folder at the Finder level is a
Messages folder (which contains each message stored
in the mailbox as a separate .emix file) and an
Info.plist file. Any other folders and file names are
left over from the import process which are not
needed by Tiger Mail but are not deleted after the
import process is complete and can sometimes cause
problems.
Does "Rebuild" delete the Info.plist and recreate it?
There is also a Eudora mailbox cleaner utility which
may be helpful here.
Yes, this is what I used to bring my mailboxes over from Eudora. It doesn't work very well and I'm in contact with the developer who has given me a beta to try and it's a little better.
Do you sleep? ;~)
Rarely. I sometimes get by on 4 hours a night.
This can be done before you go to bed which will be
completed in the morning when you wake.
I was assuming that the "Remove Envelope Index" trick was to be used when in dire need, not a nightly event. Are you saying that it should be a nightly event? Sometimes it doesn't even complete, leaving some mailboxes in the same state as outlined in my original post, whereupon I have to do the "Import Mailboxes from Apple Mail" trick from within Mail.app itself but this gets old fast since I have to move the contents from the Import(-x) hierarchy to its "proper" place in my mail hierarchy and then wait for it to "rebuild" which takes a while but nowhere as long as 5 hours. Maybe 20 to 30 minutes. But multiply that by a couple of mailboxes and my day is shot.
PowerMac G5 dual 2GHz & MacBook Pro Core Duo Mac OS X (10.4.9)

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