4mm seems like a lot of retraction for a direct drive system... you may want to try something less (my FT5 stock extruder uses 1mm)
regarding end g-code I wasn't referring to post processing, but instead in the printer profile there is start and end gcode, check there to see if there is any end of print retraction (some is ok, but you don't want too much). If you are retracting molten nylon into your break, then letting it cool, I'm not surprised you are getting clogs.
If you let it cool with the fan still blowing on the heat sink for a couple of minutes, that should be fine (I'd say get it down below 150C before shutting off).
I don't think there is any issue leaving the filament in after a print, just make sure you aren't pulling liquefied nylon into the heat break then letting it solidify.