As long as Endpoint security is starting properly and was previously working, it should start up and be running with the same policy that it was running with before the reboot.
We recently added a mitigation to help with this in the advanced policy section for endpoint that you could try setting to true. (but note that it will not take effect if Agent isn’t already running to delivery that new configuration to endpoint).
The Agent team is working on a complete fix to this issue that will hopefully be out soon (hopefully next minor, but thats not my team so I can’t commit them to that).