In Apple Mail, how can I maintaining Mailbox links when migrating hosting?

First, I apologize if this question has already been asked and answered.  If so, please kindly point me to the appropriate discussion.
I'm in the process of changing hosting for one of my (several) websites and email addresses.  I have been using Apple Mail succesfully with the site email using IMAP for several years, and have many thousands of messages, many of which that have been moved into different folders in Mac Mail locally (not the IMAP folders).  What I'd like to know is if it's possible to maintain all of these links during and after I migrate my website and all server mail to a new hosting company.  I'm very paranoid that all of my links (to mail in those boxes, and relationships to sent mail) will be lost, and that all that mail will simply redownload to the primary Inbox.
On a separate note, I'd also like to know if, once the above issue has been addressed and resolved, it's possible to copy my entire Mail application to another computer so that I can keep a mirror copy of two mail applications fucntioning like an exchange server.  Meaning, if I download one piece of mail on one computer, it will automatically be downloaded and marked as read on the other *and* if that mail is moved to a local Mail folder, if it will be moved on the other computer in the other Mail application.  Basically so that all mail and mail relationships stay in sync across multiple machines.
Hope this question makes sense.  I'm happy to elaborate, and am appreciative of any help.

Ok, so even thought no one has answered, it appears that once I move mail to the "On My Mac" mailboxes, they no longer exist on the server (though they can be moved back there if desired).  Which means that I'm fine if I migrate my hosting to a new server, and redownload them, because the mail in "On My Mac" will be untouched.  The only thing I don't know about is the "Sent" mail, but I believe those also exist on the server, and therefore if I migrate them then the link relationships are maintained (no idea about the mail that is "On My Mac" that has links to "Sent" mail in the server, but I guess that isn't so important).
As for keeping a completely syncronizable Mail application - the only way it appears I'd be able to do that is to forgo "On My Mac" entirely, and keep *all* mail on the server.  If I want to move mail into different folders, those folders would have to be Server folders created for that account, and hosted by that hosting company.  This actually doesn't seem like such a bad move, especially as we get further and further away from having only one device that we use to process Mail.
Are there any disadvantages to *not* using the local "On My Mac" folders?  Are there any major advantages to using them?

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