Rolling restarts are causing are app engine app to go offline. Is there a way to change the config to prevent that from happening?

We know that it is expected behaviour that Flexible instances are restarted on a weekly basis. Provided that health checks are properly configured and are not the issue, the recommendation is, indeed, to set up a minimum of two instances.

There is no alternative functionality in App Engine Flex, of which I am aware of, that raises a new instance to avoid downtime as a result of a weekly restart. You could try to run directly on Google Compute Engine instead of App Engine and manage updates and maintenance by yourself, perhaps that would suit your purpose better.