POP3 Apple Mail vs M-Me Mail - any conflicts? (besides bandwidth overload.)

As long-time user, with four year's traffic totaling over 10 MB of mail folders and posts (not including media or downloads), I love the idea of having it both ways:: MobileMe web access, when on the move, and traditional local storage of posts, for desktop use. There is a very large benefit to having my mail history (+ documents directory) stored by mobileme, idisk (copied manually), Time Machine, AND on my MAC mini. Many is the time I wished I had a third source of recovery from errors or disasters...
That said, there is really high overhead on re-sorting and retransmitting a whole Christmas Tree of folders and files, across clogged nets, just to search for a file or check the health of the indexes...
My question is: does MobileMe in any way affect the prior functionality of Apple Mail via POP3..?
I am worried, because I see, more frequently than ever before, glitches in the indexing of my mail folders. Searches go awry, folders are missing or folder names get moved into different sub-directories, or messages will appear in more than one directory... I am mystified.
Generally, the old reindexing feature, plus checking permissions using Disk Utility (plus getting the current OS-X update) fixed everything. BUT, with the latest upgrade, I see the new recommendation is to: "move (all) the mail files, and then ask Apple Mail to recreate all the folders" .. and their contents, by download from the MobileMe servers. This is a SCARY BIG piece of network traffic, even on 3000 KB/s Verizon DSL.
If this sounds like a 'grumpy old man', you are correct Mark me enthusiastic, but cautious.
My history includes a first programming success on an IBM 1620 in 1962, using punch cards and the GOTRAN interpreter. Later, after RPG in the Navy, I wrote BASIC on an Ohio Scientific 6502 CPU, BASIC on a Ti-99/4a... Then, BASIC & APL on Service Bureau's timesharing, and finally PERL and HTML on the net. I do a lot of 'Office', as well.
I was never really happy, until finding Karelia's SandVOX, on the mini... see: http://charitykicks.com I love my six year old MAC mini - using it, and with OS-X, I eagerly bailed out of the "you-know-what" 'world' ...
I plan to buy a new 'machine-tool-milled' mini, with all its new I/O, once the fuss dies down. Half my purchase will be software ..!
Please, please, please ... give me technical support for the idea that those of us 'early adopters' of personal computing may quickly embrace 'cloud-computing' without fear that our extensive work environments will not be held hostage to several third parties' bottle-necked bandwidth.!
Thank you,
Scoutmaster Obiwan

Long term, MailForge looks like it's going to become a worthy replacement for Eudora. Check it out:
http://www.infinitydatasystems.com/mailforge/index.html
As far as importing into Eudora OSE is concerned, I've done it without experiencing any adverse effects. It won't "take over" as long as you keep the Eudora OSE application separate from the "real" Eudora - and don't have both of them running at the same time (both trying to access mail servers etc.)

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