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This does happen with other applications, and there's uncertainty about whether it's an OS X or Atom bug, consensus seems to be OS X. I worked around it by adding the recommended commands to an alias to my .bash_profile so I can just do killdups when it happens:

alias killdups='/System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Support/lsregister -kill -r -domain local -domain system -domain user;killall Finder;echo "Rebuilt Open With, relaunching Finder"'

Reload .bash_profile with:

source ~/.bash_profile

Then run in Terminal:

killdups