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Have you noticed if it makes a difference what filament the issue happens on? You could try a cold pull and see if you can un-stick anything stuck in the nozzle. You can youtube how to do that. I guess it is best to use nylon, but the only time I did it I just used white PLA. I didn't even take my boden tube off the hot end because the connector was really stuck and I didnt feel like messing with it. (more risky though because then you can get junk stuck in the tube.) My problem was different though...the extruder would skip every once in a while during extrusion, which made it more obvious the nozzle was partially clogged. Also, What temps are you using?