I forgot about actions.

recipes/default.rb

@@ -79,7 +79,7 @@
 # The updating of the list of checks.
 ruby_block 'updating of the list of checks' do
   block do
-    checks = run_context.resource_collection.select { |r| r.is_a?(Chef::Resource::NrpeCheck) }.map(&:command_name)
+    checks = run_context.resource_collection.select { |r| r.is_a?(Chef::Resource::NrpeCheck) && r.action == [:add] }.map(&:command_name)
     node.set['nrpe']['checks'] = checks
   end
 end