I use multiple nozzle size all the time with my Makergear M2. I am also using an older version of S3D which I don't think matters as I also use Prusaslicer with the same Extrusion Multiplier.
With extrusion width you have to take into account the actual thickness of the filament you are using. Most filament I use meausures about 1.70 - 1.73 average and I set the diameter in the Other Tab to that average.
The other thing that affect it is the extrusion width. I DO NOT use auto, I set to a range depending on what I am printing but rull of thumb is .4 to .5 larger than nozzle. So makergear default of the .35 nozzle is .4, with a.5 nozzle I use .55, with the .75 I use .8 Not auto
With a given plastic once your extrusion multiplier is set correctly there should not be much change. Always check by printing a single layer square amd making sure your threads are attached to each other.
I did notice that my normal .92 -.93 Extrusion multiplier used with all 3 nozzles needed to drop to .91 when I used PLA with I don not normally use.
So to answer your question, you should always check Z offset and extrusion multiplier when you change filament or nozzle until you have documented your settings and get to know how thing work with your particular machine and filament.
For the first year I ran on the under extruded size as I wail making miniatures, when I started making mechanical parts, proper extrusion multiplier was more important for accurate size and strength, and what the part looked like mattered less.
Good luck and take notes!
Attached is .4mm square to print at .2mm height to view how your threads are adhered.
One side affect of a fixed width is that sometimes you will bet a blank line where the space is too thin, and other times a wide thread shoved in a gap that is too small. I live with that as Auto has never worked well for me. V4.01 S3D
Also when the attached square is printed it should be 4mm tall+- .02, this is checking your Z offset
- 26x26x.4 2 layers at .2.stl
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