So workbench.library from 3.1 is on those disks but you have a newer WB3.9 workbench.library is in your FlashROM on the deneb and causing the failure?
Why not use workbench.library from 3.1 in the Deneb?
I imagine the standard WB3.9 mechanism of patching KS3.1 ROM will just work?
Does patching workbench.library require a reboot you are trying to avoid?