I am having this same problem. The only thing I have changed in this profile over the last couple days was disabling z-hop when retracted. Additionally prior to finding this issue I was running a retract tower with extensions>post processing>modify Gcode>RetractTower script from Calibration Shapes from the market I have removed the script before running into this issue. I have attached some photos of a benchy where the slicer is filling in the Chimney, Deck Box and Deck.
From the printed models the red one is one printed with this G-code the green one was a prior model. g-code for the one with the fill issue included.
CE5_3DBenchy_filled in floors.gcode