The following note indicates applications services must be shutdown.
Using AutoConfig to Manage System Configurations in Oracle E-Business Suite Release 12 (Doc ID 387859.1)
Especially on multiple tier systems, you want to have autoconfig run last on the main web tier and users could get strange behavior if you try to run autoconfig while the system is up.
It is very important to follow as per guidelines.
There are cases which could lead to corruption of environment when Autoconfig is executed in Apps Tier without stopping the services.
Thanks Michael, Jibu, and ALL
Ouch! I been doing it many times the services is up, but after running autoconfig I bounce all (both apps & db)