You can make the time machine to backup only your mail folders that are already stored on your mac and are updated daily when the emails arrive. In case you are wondering where are your mailboxes then you can find them here:
Apple mail mailbox location:
1. Open a new Finder window
2. Go to your home directory using the Home toolbar button or select Go | Home from the main menu
3. Open the Library/Mail/Mailboxes directory
This will open up the correct directory where your Mac Mail stores emails. Usually this directory is called Mail and contains multiple sub-folders named the same way as your email accounts. POP accounts and IMAP accounts are named with prefix POP- and IMAP- respectively. Each account folder contains multiple sub-folders for your Mac Mail folders such as Inbox, Sent Items etc.
The folder called Mailboxes is the main storage for your emails. You should copy this folder including all subfolders and files inside to the Windows PC and use it as the Source Folder for the Mac Mail to Outlook Converter.
Take the following steps to open the folder where Mac OS X Mail v1 keeps your messages:
1. Open Mac OS Finder application
2. From the main menu select “Go” item
3. Choose “Go to Folder…” menu item (You can also press Command-Shift-G).
4. Type in “~/Library/Mail/V2” (for Mac OS X Mail 5-8)
or “~/Library/Mail/V3” (for Mac OS X Mail)
This indicating the location of the lication of the Mac Mail v1.0 mailbox. You have to use this folder as the source for the conversion.
Outlook 2016 for Mac database location:
Outlook 2016 for Mac stores messages and other items, such as calendar events, contacts, tasks, and notes, as a SQLite database in the /Users/username/Library/Group Containers/UBF8T346G9.Office/Outlook/Outlook 15 Profiles folder.
If you turn on Time Machine, it automatically makes copies of every file on your computer on a regular basis. If a file gets damaged or lost, you can use Time Machine to browse through the backups and recover the copy of the file.
You can include Outlook data from your Time Machine backups by adding the previously mentioned folder to Time Machine's item inclusion list.
However there are third party apps also available that are capable of backing up emails database of various email clients. One that claims to backup every email client on mac is Mail Backup X: http://www.mailbackupx.com/
Choose your solution wisely.
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