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I've had this happening to me too. Sometimes because of too many retractions per mm of filament. This caused the filament to become flatter and eventually get stuck either right after it exited the extruder or in the e3d hotend at the heat break. My solution to this problem is to limit the "Maximum Retraction Count" and "Maximum Extrusion Distance Window" in Cura to around 30 times/3 mm and it solved my problem.
Another possible source of the problem is over extrusion but that's probably not your case since you only experience the problem when you print with lots of retractions.
Yet another source of the problem is excessive retraction distance which causes the retracted filament to cool down and harden above the the heat break and thus blocking the hot end. This happens in e3d v6 hot ends especially as the heat break becomes narrower. The filament looks like a spiral with a thicker end when you pull it out of the hot end.
Printing too close to the previous layer can also create too much back pressure in the hot end and cause the extruder to skip steps and flatten the filament in the process.