I'm thinking of another extruder on my printer, and I'm curious about this one....
Is it necessary to have both hot ends on same height? Why yes / why not? (if there is not)
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I have a dual extruder Replicator 1 and having the nozzles at the same height is a must and albeit a bit of a struggle otherwise. At one point, I had to disassemble my extruder head and the nozzles didn't line up quite right. There after, printing with the lower one obviously didn't have any troubles, however, printing with the high extruder made it so the lower extruder would scrape the molten plastic layer. This made my surface finish horrible and almost impossible for support structures to be printed.
Instead of fighting with my stock nozzle assembly to get everything perfectly lined up, I just shimmed the one side with some stacks of paper cutouts. This brought my extruders very close to even.
Also, you'll want to make sure excess plastic is cleaned off of BOTH nozzles when printing with either nozzle. I found that some prints would fail because of a small discharge from a previous print on the other nozzle.
I don't have dual extruder printer myself, but to my understanding having both nozzles leveled at the same height is critical for getting successful prints.
For typical FDM printers, the lowest point of the end effector should always be the nozzle. If you, for instance, mount a fan lower than the tip of your nozzle, it will eventually collide with the printed object.
The effect of having unequally leveled nozzle tips for a dual extruder printer will be exactly the same: one of the nozzles will either drag against or collide with the model during print; or, one of the nozzles will be to far away from the model, giving poor layer adhesion. Either way, the result will be sub-optimal.
So, leveling both nozzles equally is probably a good idea. You might want to have a look at this question on some advice regarding how to do it.
If your printer has no way to move the heads up and down, or otherwise out of the way, and your slicer isn't able to detect collisions and account for head height differences in the produced G code, then they must be at exactly the same height from the bed.
If extruder A is hanging lower than extruder B, then when B has printed at a certain level, and A moves across that area, A will hit the material B has printed.
Unfortunately, this is further complicated for newer printers because some of them rely on digital bed leveling. If your bed isn't parallel to your X and Y axis movement, then you have to work very hard to make sure the heads are parallel to the bed, and with some mechanisms this isn't possible without making the mechanism itself parallel to the bed, so just mounting the new head at the same height as the other head might not be sufficient if your printer isn't perfectly calibrated already.
I have not yet seen a printer or slicer that manages heads of different heights, but I suppose it's possible to manage the problem with additional intelligence. For instance, if the printer can move the heads up and down independently, it might move one down for printing, and the other up and out of the way when it's not printing, and then the opposite when it switches. I can't think of a good reason to do this, though.
Another option would be to develop a slicer to generate G-Code that will prevent such collisions. The printer would necessarily be limited in what it could print depending on the location of the second head, as there are some situations where it would need to print in a certain area, but a collision prevents it from getting to that area.
At any rate, no one has developed such software or mechanisms yet, so if you had good reason to mount the heads at different heights, you'd have to account for all of these factors and develop the complete solution yourself.
To add to the above answers, besides the obvious point that one hotend might collide with something another hotend positioned lower than it has printed, you also want both hotends to be positioned X microns above the bed at minimum height so your filament will stick to the bed properly. Position one a bit higher than the other and what it prints won't stick to the bed very well, position one a bit lower and it will hit the bed and clog/be unable to print the first layer. The only reason I can think of when you'd want one hotend to be higher is a situation when you're not using both hotends and don't want the second hotend to drag on and deform a layer the main hotend has printed and is still warm and deformable. If that's an issue (I doubt) then sure, move it a bit higher.
If there are other reasons for what you would like to have the hotends at different heights, please add that to your question. I can't think of one myself.