If you have a backup, the following won't be needed. But here goes:
OK, first let's make backup copies of those two Mail folders. Select/highlight "Mail(original)" by holding down the Option key while dragging it out to the Desktop and letting it go once it's there. You should see a small green plus as you do make the move. If you don't, then stop, don't drag it out and let it go. Try again until you see that. Next do the same for the new, small one.
Important: do not change the names of anything. Leave Mail as "Mail(original)" both in the backup and in its original location.
Next, back to the Applications folder -- or wherever it appears -- for those two, not the copies. Select/highlight the small, new Mail and right-click (Control-click) it to show Package Contents. When the Package Contents appear, click on and open all the disclosure triangles in front of the folders that appear (the folders will show with a folder icon.) Leave all that open.
Next, open the Package Contents for "Mail(original)" But no need to click the disclosure triangle on anything except Contents. You will have both Package Contents for both "Mails" open at the same time.
Now, from "Mail(original)" move/drag the entire Resources folder in to the new, small Mail that only appeared with the update. It goes down at the bottom just below the Plugins folder. That's it, except be sure that this new merged Mail is in the Applications folder inside the Macintosh HD folder, sitting by itself and not enclosed by another folder. If there is an enclosing folder, trash that.
When that's done, close up all the triangles and close those windows.
Now select "Mail(original)" and move it to the Trash. But, important, DO NOT empty the Trash.
Next, open Disk Utility and repair Permissions for the boot volume. That's the one indented below the first listing showing the drive and manufacturer. (I'm not sure this step is absolutely needed, but just in case.)
When it's done, inspect the resulting messages to see if Mail is showing as having been repaired.
Now, for the moment of truth. Try to open Mail from the Applications folder, not the Dock. If it doesn't open, back to the drawing board.