How to deal with multiple mail files?

Here's the story; it's sad but true: After a failed iSync spirited away all of my emails, the Apple Care techie I spoke to a month ago wasn't able to fully resolve the problem. So, currently in my Home Library folder I have 2 Mail files: #1 is labeled "Mail" and #2 is "Mail Copy."
"Mail" has one sub-folder called "Mailboxes" and four other folders for each of my four POP email accounts (there are also a number of other files that I'm ignoring for the moment like--Envelope Index, Signatures.plist, ect.). All mail from the past 4 weeks is in the folder labeled "Mail." But...
The other folder in my home library--"Mail Copy"--contains 3 POP email accounts and each one has sub-folders that contain mailboxes with my emails that go back many months. I want to keep the email in both folders, "Mail" and "Mail Copy."
Problem: How to get the older messages out of "Mail Copy" and back into the current "Mail" folder. Clearly, it would be a mistake to simple drag them from one location to the other, since the "Contents" files and ".plist" files wouldn't match.
I would be extremely grateful for any guidance the Mail authorities who contribute to this forum might be able to give.
Also, for the life of me, I cannot figure out where the emails actually reside. The "Mail" folder contains a subfolder entitled "Mailboxes" and it contains subfolders for each mailbox like "Action.mbox" and "Hold.mbox." Then, inside each .mbox folder are other files and usually one folder. Most of these files have names like "content_index," "Info.plist," "mbox," and "tableofcontents." And there is a folder labeled "Messages" and it contains numerous ".emix" files and one "tableofcontents file." My confusion begins when I open a particular POP account folder and find .mbox folders also located there and those folders also contain .emix files. I've searched the entire knowledge base, and I find no explanation anywhere of which files/folders are located where and why.
Many thanks for your time and trouble, Jay

The easiest way to combine the old folders with the new is to use the "Import" option in Mail's File menu. Consult the Mail Help topic "Importing email into Mail" for comprehensive instructions for doing that. In your case, the "archived" messages will be the ones in "Mail Copy."
The actual messages are stored in individual *.emlx files, inside each mailbox folder's "Messages" folder. (For instance, you would find a message in a locally stored, root level mailbox "Action" at path ~/Library/Mail/Mailboxes/Action.mbox/Messages/xxx.emlx, where "xxx" is a number.)
Some of the files you mention are leftovers from Mail 1.x & are not needed with Mail 2.x. They won't do any harm if left in place, but you can remove them if you wish. (I suggest making a backup of the entire ~/Library/Mail/ folder beforehand, in case something you need accidentally gets deleted.)
These files are not needed by Mail 2.x: "content_index," all "tableofcontents" files, & files named "mbox." All folders with names ending in ".mbox" are needed, since they contain the .emlx files. You may also find folders in ~/Library/Mail/Mailboxes/ with no ".mbox" extension pared with folders of the same name with the ".mbox" extension (like "Hold" & "Hold".mbox") -- do not delete any of these, as they contain "Messages" folders as well.

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