In Font Book 2.2.1, I resolved font duplicates and all works as designed. I have operated in this mode for several months, so I presume I do not need the duplicate fonts.

The duplicate font is greyed out as it should be.

When I Control Click on the greyed out font, I am given the option to remove the disabled font.

So the question is, should I go ahead and do this? What else should I do to clean thing up?

FWIW, I have not specifically added fonts. I only have those that came with the OS and applications that I installed.

you may want to see where each one is.

More than likely the duplicates are such as one in /library and one in ~/library. in which case should be safe to remove from your home.

probably don't want to remove fonts from /library