Hey, I had a similar issue with under extrusion, and with very extensive trouble shooting, it turned out to be the extruders throat tube that was a bit iffy. I had upgraded to a E3D v6 hotend, I replaced my extruder assembly, nozzles, tried varying temperatures on the filament, and made sure the nozzle was properly hot tightened, amongst many other maintenance checks (belt tensions, rollers tightened etc).

A good test I found to see if this is a cooling issue was to completely disable retraction and see if this would stop the block. This would mean completely cleaning out the nozzle, heater throat and bowden, and see if you can get a successful (albeit messy and stringy) print. This could identify if this is a cooling problem with the filament somewhere or if there is a hardware block.