Missing pipeline jobs with Warning : Configuration Reload

We see the pipelines goes missing without any restart or changes on the application or backend with warning

Trigger Time Message
hudson.triggers.TimerTrigger Jul 14, 2022 11:31:49 PM Trigger hudson.triggers.TimerTrigger.run() triggered by org.jenkinsci.plugins.workflow.job.WorkflowJob@XXXXX[] spent too much time (48 sec) in its execution, other timers can be affected

Jenkins initialization has not reached the COMPLETED initialization milestone after the configuration reload. Current state is: “Augmented all extensions”. Such invalid state may cause undefined incorrect behavior of Jenkins plugins. It is likely an issue with the jenkins initialization or reloading task graph. Example: usage of @Initializer(after = InitMilestone.COMPLETED) in a plugin (See documentation). Please report a bug in the Jenkins bugtracker.

Can any one help me here?