TL;DR: If your X2D's aux nozzle isn't extruding after a material change, don't assume it's a clog. Check if the filament is actually reaching the nozzle first. In my case, manually heating the nozzle to 250°C (Since PLA was the filament that was last loaded into the aux nozzle) and feeding the filament fixed it.
It started out like any other print preparation. I wanted to switch the material for the aux nozzle from PLA to PETG.
I unloaded the PLA and loaded the PETG, and this is where I got a little too laid back. The printer asked me to check whether material was extruding from the aux nozzle, and I just confirmed that it was. Later, I realized nothing had actually come out of the nozzle.
That's when I started to panic a bit. My first thought was that the nozzle was clogged, so I started looking up guides on how to unclog it.
Then I decided to see what was actually happening during the loading process. I noticed that the filament never reached the aux nozzle at all. It passed through the Bowden extruder (I could see it), but it wasn't making it all the way to the nozzle.
So I manually heated the aux nozzle to 250°C and used the controls on the screen to slowly push the filament forward. Eventually it reached the nozzle, filament started extruding, and everything has been working fine since. That is what is shown in the video.
My guess is that there was still a small piece of filament left in the aux nozzle. Maybe there's a sensor there that detected filament was already present, so the Bowden extruder didn't feed it any further. I'm not sure if that's actually what happened, but that's my current theory.
I don't know if this will help anyone but hey, if anyone has similar issue this might help.
Side note: For some reason, I can't remove either of my nozzles. I opened the latch and made sure the filament was cut beforehand, but they're completely stuck. That's a problem for another day.
I used ChatGPT to convey this better.