I recognized that the second hotend is also heating up to printing temperature even if it is not used for printing. This is similar to the problem of the second filament sensor sending a "runout" even if no second extruder is used for printing...
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I use Simplify3D, I use a single extruder protocol if I only want to use one for that print job (and unplug the solenoid). For dual filament jobs I created a Dual Extruder protocol.
So either one heats or both heat.
I have no experience with Cura, but I’m happy and still tuning my processes.
yes, both runouts have to be loaded if plugged into touchscreen. Possibly if they were plugged into the main board this could be resolved but I believe Marlin currently has issues with this.