When I go to create a g-code in prusa-slicer, the stl I'm using shows up with missing layers when I slice the file. I've gone over the file many times in rhino and made sure its a closed object, so I don't know what's wrong.
Engage Crystal Ball
it would be useful to have more info...
try slicing for a 0.25 nozzle,
if the layers reappear, chances are the wall is too thin.
in this case you could try adjusting the XY compensation value to 0.1mm, or 0.2mm
this will artificially thicken the model components
other options are, increase the model scale, or
re model the parts which are defective
Could be a million things. It would help if you could post the STL or ideally a zipped version of the 3mf project file out of PrusaSlicer.