I'm just going to put it here just in case.
Is this filament flattening significantly through the filament driver mech?

I have this issue due to a fixed gap at the driver. All works wonders until that one print that does a lot of retractions. The filament that rides back and forth in the driver just flattens, and widens the filament.

How much flattening will our bowden tubes tolerate? That depends on the bowden tube. I now make sure my bowden tubes are at least 2mm ID. I push a bike spoke through the tube and it get stuck, the tube is too small.
Haven't had an issue since.