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I just confirmed that the file that is uploaded has no holes in it.

Some things to try:

  • Make sure to try the latest version of the slicer.
  • Use a visualizer to view the STL before and after Slicing.
  • Try slightly different slicer properties, like layer height or wall thickness.

I suspect the Slicer is having a problem with something in the model. I have ran into some strange issues with slicers when the models are a little complex and detailed. Often the issues get resolved with the next release of the slicer. But it is a good thing to bring this issue to the people who created the slicer so they can diagnose the problem.

I use Cura myself; it has nice visuals to not only see the model but also see the layers after slicing.