Making configuration changes and restart

I have alertmanager and prometheus running on aws ec2. Whnever i make a chnage to alertmanager or prometheus yml file, and restart the services, i see my alerts firing count resets. thi sis really annoying as, i have long running alerts (e.g. for 4w ), after restart they all go to pending from firing and i have to wait for long time. Is there a preferred/better way of restarting? I tried reload cli but it is behaving the same.
Thanks in advance