The Extrusion Conclusion
This is a story of hot ends, jams, extrusion and changing filament in my Micro Swiss hot end.

Investment in an all metal hot end was one of the very first purchases I made for my 3D Printer. It allows me to run a higher temp and generally speaking is not subject to issues with a Bowden tube being millimeters from your heater block. The Micro Swiss was performing as I had hoped for quite a while now and it was not until I started printing sample cards for an upcoming video that I ran into this problem. After some outstanding support from Micro Swiss and back tracking through my steps I was able to solve an intermittent problem with jams on my printer.
The problem went down like this. I was printing these filament swatch cards and for the most part things were going fine. I would complete a print and change filament and then print the next. Occasionally throughout this process I would run into a jam or clog or something but at the end of the day I was not able to load new filament. Most of the time I could help the extruder push through the problem by applying some force in addition to the extruder. I figured at that time something was just not lining up with the filament going in. Usually cutting the filament differently would fix the problem.
Then one morning I woke up and went to change the filament after a night of printing and I was stuck. I could not for the life of me clear out the problem. First attempt was the old needle in the nozzle (does this ever work?) which did nothing. I next took out the nozzle completely and found there was very little filament in it and could not possibly be where this hang up is. So I reached out to Micro Swiss who was very helpful. We covered possible alignment issues, having things flush and details about the inside of the hot end. Sadly they had never heard of the nozzle doing this either. So I was sure I was hitting some edge case.
My next step in fixing this issue was to see if I could insert something from the hot side into the cool side. So I chose a very small precision screwdriver (Sure, screw drivers jammed into this always work!) and I was able to insert it far enough into the hot end I felt resistance. Seeing as I did not want to break my heat brake (yeah I said it) I started by turning slowly and then pulled out the screwdriver. I found it covered in the filament I had in previously. Which was a curious thing given that the heat brake should not contain residual filament. So I attempted it again and with a little pressure was able to free my clog. The only thing that came out was the previous filament color. So this was strange and I thought for sure I had significant problem with cooling. So checking the fan and reading the temperature I was running way below the 60c glass temp of most PLA. So what caused this?
Retracing the last couple of clogs I'm convinced that this issue is being caused by the cool down process post printing. Normally the heat brake keeps the heat out of the cool side of your hot end. On a longer print the hot end and heat brake get a tad warmer than they do say when you first heat up your printer from a cold start. The fan keeps things cool but your heat break is going to be at its highest temp right after a print completes. This is where I believe the problem lies. At the end of the print the heater block stops heating and slowly cools down. The cool end stays cool but is now sending that cool ness from the cool end down towards the hot end. The heat brake though is going to be warmer at this time and I believe what happens here is that some filament is transitioning to the glass temp in the heat brake during cool down. I believe this is also either sticking to the wall or the small microscopic gaps where the pieces meet. This is generally not a problem because when you heat things back up and push more filament out it gets cleared out. Normally though you're flowing just in one direction, from the extruder to the print bed. Occasionally however you go the other direction which is to change your filament.
This direction change is where I think the problem happens. The print ends sometime in the night, some filament sticks on the inside and then the next day I heat it up and do a filament change. The difference though is that those microscopic pieces in the heat brake now work like a scraper grabbing hot filament on the filament change. Because they are cooler (because I haven't been printing for say an hour) they stay in place but now grab hot filament on its way back out of the hot end.
I was able to reproduce this a number of times. The solution was so simple. I now extrude about 30mm of filament before a filament change if the nozzle was at a completely cold state. Since I added this extrusion before the change my problem has disappeared completely. This clears out anything from the previous print that was heated up and every filament change is now flawless.
Micro Swiss agreed this sounded like something in the heat brake partially transitioning its glass temperature. They agreed that this process " will also help to prevent form heat moving upwards and sticking to side of the tube in cold zone". So there you have it. If you're getting clogs while changing filament try this one simple trick (yeah I said that too) to prevent them in the first place.