There has been a behavior change in Path>Flatten in v1.4 compared to v1.3.2 that might cause a few headaches. V1.4 will will also convert the strokes to paths that may introduce additional profiles in Fusion that may not be wanted in your designs. If the stroke width is very small (1px?), you may not even understand why your designs are failing. 

It is my understanding that this behavior will be permanent and not changed in future versions of Inkscape.

The fix? Simply set the stroke width to "none" (Remove Stroke) then proceed to do a Path>Flatten. After that you can set the stroke to whatever you want. 

 

This might also apply to Cricut Design Space, Blender, LaserGRBL - etc etc etc etc etc 

Wow.  

Thanks for posting!

Yeah - I had to post this to save other makers a nervous breakdown. 

Took me quite a frustrating  time to figure out what was going on. Bodies wouldn't combine properly in Fusion. Error city. Since I normally just use a 1 px stroke in Inkscape, I had to zoom in like a microscope in Fusion to see the double profiles because of the ~10mil difference. Then I had to figure out what was causing that in Inkscape. Once I discovered that, I went back to v1.3.2 to verify if the behavior changed. Yup - sure did! Undocumented behavior change. 

I just got lucky in figuring it out. It could have been a billion things. Did I accidently do a stroke to path???

Crossing my fingers in hopes the developers don't apply the same logic to the Shape Builder tool, Fracture and the boolean operations. Since the Shape Builder tool was introduced, it has become my #1 path tool.