The temperature-controlled (integrated and not removable) stainless steel tank in my ultrasonic cleaner doubles as a sizeable soaking tub. For really difficult cases, I would start with a three- or five-minute cleaning cycle, then just leave the pen components (nib, feed, housing, converter, cap, or whatever needs cleaning) to soak for anywhere from ten minutes to hours at 32° Celsius, then run another cleaning cycle, before transferring the components to the sink for flushing with plain water using a rubber syringe bulb.
The only pen components I've ruined by doing so are the parts of the wooden pen body on a Moonman M6. I gathered that the dilute ammonia solution in the tank completely stripped the coating from the wood, and the wood itself get saturated with water and swelled up, to the point that the cap would not screw back on properly. It took about three days for the wood to dry out enough for it to return to normal size and the threads to fit again. I haven't used the pen again since, though, because even when the coating on the wood was intact, the cap was still very ineffective at preventing ink evaporation, so until I can (be bothered to) find some suitable wax to apply on the wooden body, there is just not much point in filling the pen, especially I don't really like using the nib on that pen that much.