What version you have may matter. I have not used it in a while so this could be a bit out of date. However, in the past once you set them manually they were generally sticky upon remeshing. Geometry changes would affect the parts/surfaces in question and you might have to manually re-align. There is also an option for automatic alignment of non composite shells in the options. I usually turn this off as it takes much much longer launch a job when this is on and it does a worse job at aligning shells than with it off. Try that those things and if it still doesn't work that well an enhancement request is your only other options as far as I know. And. this option doesn't really work very well. The issue I believe is that SWX itself does not track surface normals so it gets a bit tricky, as do most things in shell meshing in SWX Sim - not its strongest suit in my experience.