Screw holes merged into a long gap in the gcode (and print)

[PropellerHat]

Hi

We are printing a huge box shaped thing that consists a bit more than 1000 layers (0.4mm). Now when arriving to the print site I see in one side of the box an opening that was not in the STL file that I imported into S3D. There were meant to be 2 holes of 2mm for screws, and Simplify3d has merged these holes together leading in a long gap. When checking the ready gcode I see the part of the print missing. Why didn't I check it before printing? Because of the more than 1000 layers I checked only the areas where to expect issues, not the plain walls.

Does somebody know what is causing this? Is there a way to check the differences of the gcode compared to the stl, other than "manually" examining every layer?

Thanks!

[CompoundCarl]

That usually means there is something wrong with the mesh. If you want to post your factory file, others can take a look and try to confirm (File > Save Factory File).