You may not have a fan issue at all… this is possibly a defective thermistor, loose thermistor or heater core, or loose/damaged wiring.
Once upon a time, a 3D printer could burn your house down. Here’s how that worked…
The board calls for heating up the “hot end” of the extruder … but not indefinitely… only until it reaches the desired print temperature. It knows when it hit the desired print temp because there’s a sensor (thermistor) which reports the temperature back to the board so the board knows when to stop heating. The board basically cycles the heat on/off on the hot-end to keep the temperature hovering very close to the desired printing temp.
If the terminator fails, the board thinks the hot-end is still cold… so it keeps heating… and keeps heating… and it never stops until things get so hot that other things start catching fire. (not good)
To save you from this situation, the printers firmware monitors for this. Basically it has a good idea how long it should need to call for heat to the hot end and should see the temperature heating up as needed. But if it has been calling for heat for a while and yet the thermistor doesn’t report that it has achieved the desired temperature, the firmware gets suspicious that the thermistor is defective … and shuts down before your house catches on fire. It reports this to you as … a Thermal Runaway.
Here’s a document that shows how to replace the thermistors on a dual-extruder printhead (I realize this isn’t the printhead you have … but LulzBot doesn’t seem to have a document specific to your printhead and this process will be very similar.)
BTW, regarding those fans…
On your printhead there are two kinds of fans. One type cools the part (you have two of them – left and right – and they are aimed at the nozzle). The other type blows air on the heat-sink of the extruder’s “cold end” to prevent heat-creep. That fan (extruder heat-sink cooling) is normally always on and you can’t change the speed.
The parts-cooling fans can be controlled in your print job. It’s very common for most filament to call for no fan on layer 1 and then slowly ramp up the speed through the next several layers.
E.g. if I print PLA, I see 0% fan on layer 1, then 25% of layer 2, then 50% on layer 3, and and so on until it hits 100%.
But some filaments are different and call for less fan. When I print TPU (NinjaFlex) it uses no fan on layer 1 but the ramp-up only reaches a top fan speed of 10% (TPU doesn’t like a lot of fan). When I print PolyMax PC… that material calls for no fan at all (on any layer).
When you set the fan in Cura … it’s the part cooling fans that are being controlled (the extruder cold-end fan is normally just always on).