I've seen some similar posts but nothing about this exact case.
I have a two-color model where the one of the colors is only on the bottom few layers. But since I want it to print first (it's text, so I want it clean) I assign it to the first Extruder 1 in Cura 3.6 and the main color to Extruder 2. And yes I know you recommend Cura 3.2-3.3 but I want all the new features.
When I printed it, the print failed on an early layer, airprinting the rest. Observing the printer I found that the hot end was set to 0 degrees. The printer's failsafe kicked in and the extruder stopped pushing filament because the temperature was too low. But it kept moving the head around.
I found "M104 T0 S0" in my gcode around layer 12. Obviously Cura recognized that that color would no longer be needed, so it shut down that extruder -- the first extruder -- to prevent it from blobbing and to save energy. What it didn't know was that it shut down my only extruder!
Chroma did not remove this command. I've seen mention that Chroma does remove some M104/M109 but I'm not sure how true this is and what exactly it removes. I also know your Cura/Chroma setup instructions include setting the standby temps and such since those can cause issues with pausing and blobbing, and even failing on some printers that don't like commands on nonexistent extruders. But this is a really big one that Chroma missed.
I looked through all the Cura settings and didn't find one to disable this behavior. I tried some workarounds with extruder start/end gcode, but nothing worked. The best thing I came up with is a post-processing Search and Replace to comment the command out.
Extensions -> Post-Processing -> Modify G-Code -> Add a script -> Search and Replace
M104 T0 S0
; M104 T0 S0 ; disabled hotend shutdown
I believe this should be filed as a Chroma bug, because it seems like something Chroma should take care of, but I thought I'd throw it out here first. If it's already supposed to do it, I can submit my gcode for analysis.
I also suggest adding the Search and Replace to your Cura/Chroma setup instructions. My use case doesn't seem that obscure, and I haven't seen any recommendation that the last color to print always be assigned to the first extruder (which would also avoid this issue).
BTW I haven't seen a lot of discussion of this issue, but there are a handful of reports, such as on other multi-extruder single-nozzle machines using Cura: https://github.com/Ultimaker/Cura/issues/2918 .
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