Issue with MacOS 10.12.6, Mail Version 10.3 (3273): I don't want to view messages organized by conversations. I go to "Preferences" > "Viewing", I untick all boxes in "view conversations". My e-mails still appear organized by conversations. In menu "

Might be a corrupt .plist.

Do a backup, preferably 2 backups on 2 separate drives.

Quit the application.

Go to Finder and select your user/home folder. With that Finder window as the front window, either select Finder/View/Show View options or go command - J. When the View options opens, check ’Show Library Folder’. That should make your user library folder visible in your user/home folder. Select Library. Then go to Preferences/com.apple.mail.plist. Move the .plist to your desktop.

Restart the computer, open the application, and test. If it works okay, delete the plist from the desktop.

If the application is the same, return the .plist to where you got it from, overwriting the newer one.

Thanks to leonie for some information contained in this.

When you open apple mail application take cursor on top menu bar view > click on expand all conversations it will show all conversation with you and the recipients , that you have sent a mail to them or received from them , its just exchanging of mails , but as soon as you click on collapse conversations they will get merged .

Also the conversations goes to default settings when you quit apple mail application , the expanding of conversations can be viewed only when the mail application is opened .

And if you open mail preferences > viewing its settings are not to be changed see this article Mail Viewing preferences on Mac - Apple Support