No need for soft-rebooting to apply updates.
Upon booting, AmigaOS 3.9 runs a SetPatch command to patch the 3.1 ROM in RAM with new modules. The "Kickstart 3.9" is a community-created hybrid ROM (512KB) that combines the core 3.1 ROM with these "Rom Updates" from AmigaOS 3.9, allowing the machine to boot directly into a fully updated state without needing to patch at startup. amiga kickstart 3.9 download
The Amiga Kickstart is the that initializes hardware. Most Amigas run on Kickstart 3.1. When AmigaOS 3.9 was released in 2000 (after Commodore went bankrupt, published by Haage & Partner), it was designed to run on top of Kickstart 3.1. No need for soft-rebooting to apply updates
If you don't have an EPROM burner, you can achieve the same results using utilities, which load the custom ROM into RAM at boot: The Amiga Kickstart is the that initializes hardware
This ROM is generally intended for 68020+ processors (A1200, A3000, A4000) with at least 6MB of Fast RAM. How to Create the Kickstart 3.9 ROM (The Legal Way)