I restarted my Mac (OS X 10.11.6) this morning and upon opening Mail.app (9.3), most (all?) of my display preferences had been reset. Very annoying! I have a Time Machine backup - what file(s) do I need to restore to get Mail back to where I like it? Thanks much!
~/Library/Preferences/com.apple.mail.plist would be the first one to try.
Turns out it was
~/Library/Containers/com.apple.mail/Data/Library/Preferences/com.apple.mail.plist - restoring that did the trick.