You can disable health rules during these windows, by going to the Health Rule(s) and under Overview and ''When is the Health Rule Enabled?'' you can uncheck the ''Always'' check box and select when the time frame is you do not want this health rule to evaluate your application.

You can also put in the following -D flag in your domain.xml to have a delay in the evaluating of the health rules after start up. Here the delay is 10 minutes.

-Dappdynamics.controller.health.rule.processing.startup.delay.minutes=10