Emojis appear on some parts of apps but show as question mark in other parts For example, on Messages.app, the sidebar with recent contact list displays Emojis but the message pane does not:



In Safari, some Emojis appear on sites but not other sites. Furthermore, on sites that Emojis don't work in Safari, they work in Web Inspector:



How do I fix this short of reinstalling Mac OS?

I'm on MacOS Mojave 10.14.2 (18C54). I believe it started happening since update to 10.14.1.

I've tried the Font Book > Restore Standard Fonts..., validated the fonts but not luck.

Firefox displays emojis fine.
I had to reinstall Mac OS. I did this by pressing Command+R on reboot and then it present a menu. You chose Reinstall Mac OS and it'll reinstall it for you.

I did a backup before doing this reinstall using TimeMachine and an external drive because I thought I was going to have to restore everything again.

Good news is that I didn't have to at all. All my files were intact and the emoji issue was fixed! 

Here's more info on this type of install.