aws-codedeploy-agent: Codedeploy Agent missing gem all instances broken.

So out of nowhere today we started getting failed deployments on the vast majority of our servers.

Looking at the instances and the codedeploy agent I see:

/etc/init.d/codedeploy-agent status
Bundler could not find compatible versions for gem "gli":
  In Gemfile:
    aws_codedeploy_agent was resolved to 0.1, which depends on
      gli (~> 2.5)

Could not find gem 'gli (~> 2.5)', which is required by gem 'aws_codedeploy_agent', in any of the sources.

The codedeploy agent is dead. Manually going into the directory and doing a bundle install and rebooting the machine fixes it. But rebooting our entire AWS account is kinda a pain in the butt.

When I restart the agent after running bundle I see access denied messages until the box is rebooted. Anyway to fix atleast this part without rebooting?