Ok, so I tried a number of things and did some experimentation.
First, I went through history to find what holes were causing the issue. Turns out there were four holes that were causing the DXF export to freak out. The holes that were causing the issue were generated using a sketch within a child component. To do this, I backed up my history until the DXF import worked, then suppressed the features that were causing the issue and fast-forwarded my history to make sure nothing else was causing issue. It turns out holes punched from sketches on the same component (even holes punched from sketch in copy A through to copy B) work just fine, the issue happens when you punch holes through different components. It would be appropriate if I were to name these components for you so you understand. The "Barrel" component has a motor mount on it, we'll now call "Mount." Anyway, the sketch was in the Mount component. At first I had holes bored through the Mount and Barrel. I deleted the holes through the Barrel, and re-bored them only through the Barrel (Mount was unaffected) but that still didn't work. So what I ended up doing was creating sketches in the Barrel, projecting the holes through from the sketch in Mount, and boring from there. This worked and now I don't have problems exporting the DXF file.