Missing Inner Perimeter for a Roof

I have been struggling lately to successfully print on a new printer. However, my most recent issue seems to stem from Slic3r. As seen in the attached image, a roof is drawn over half of the infill to create a "stair step" shape. Slic3r does not generate a new perimeter for this layer. Instead, it connects some of the honeycombs along this edge, but not all. This results in the printer attempting to lay sections of the new roof over empty space. As the new section has nothing to adhere to, it is simply dragged back with the nozzle. This creates large, curled up defects that the print head inevitably collides with, often hard enough to cause layer shifts.

Am I missing a setting to generate a proper perimeter before the roof is printed?

How many top layers do you use?
In my slic3r Prusa edition, there's an "extra perimeters if needed" checkbox. Might help in your case....

Just 2 top layers. Had some holes so I plan to bump that up to 3 anyways. However, the slicing defect still occurs when I changed it to 3. Also, I have the extra perimeters checkbox already checked, sadly it did not fix the issue.

I've been using a 0.8mm nozzle, so I think the next thing I'll try is reverting back to the basic 0.4mm nozzle and see if the printer can just ignore the issue.