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This feels similar to something I saw . The PE server gets confused if it's not running the environment 'production'. Those classes think they belong to that environment. The absence of 'production' essential orphans them which is why they appear to be crossed out. If you're using Code Manager it will remove any environments from /etc/puppetlabs/code/environments that are not defined in your git repo. Which is most likely what happened here.
Oddly enough PE will recreate /etc/puppetlabs/code/environments/production on new JRuby creation:
pe_install::install::classification::pe_node_group_environment
per
https://puppet.com/docs/pe/2019.8/installing_pe.html#configuration_parameters_and_the_pe.conf_file
Good Luck,
Mike
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