OK, solved it now. Ignoring the fact that I'm using a Duet V0.6 and reading the documentation for the Duet 2 family:
https://docs.duet3d.com/Duet3D_hardware/Duet_2_family/Duet_2_WiFi_Ethernet_Hardware_Overview#inputoutput
There's a table on that page listing logical Logical pins (RRF 2.x) against Pin names (RRF 3.x) and that gives fan[0-2] mappings to the logical number range 20-22.
So by adding the following to my configuration file:
M106 P0 I-1 ;disable normal FAN0 operation
M571 S1.0 P20 ;Set 100% output to FAN 0 on extrude
It's all sorted now. I guess the firmware was transitioning to version 2 around this time and the logical pin numbering was already in place but not fully documented? Panic over anyway.