The AmigaOS 3.9 ROM update is installed to "DEVS:AmigaOS ROM Update". It will not be used if you rename or delete it. It's installed by a new for AmigaOS 3.9 C:SetPatch (version 44.38) which is executed at the beginning of S:Startup-Sequence. It can be skipped. My SetPatch line is "SetPatch NOROMUPDATE QUIET". I disable the MAPROM and use BlizKick to put a custom kickstart in MAPROM.
My next project is to build a custom kickstart containing all the patches I currently load from the startup-sequence into a ROM to flash into my Deneb.
Oh so many projects, so little time!

@Rob,
I've just sent a reply to your email you sent earlier today.