How to configure services within Systemd that can be restarted outside of Systemd?

Issue

• I have created a systemd script for our environment which starts and stops the processes fine with a server reboot. Daily we restart some of those processes with a separate script which causes systemd to think the service status is inactive. Is there a way to force systemd to run a stop of the service even if it thinks the current status is inactive (dead)?

• Is there a way to make systemd understand the processes are still active (running) even after a separate script has restarted the processes?