Yes, immersion is not a good idea, generally. Immersion and the ultrasonic itself are unlikely to harm the pen (provided no part of the pen contacts the metal tank, only the plastic basket), but it may permit water to wick into areas where it is in contact with metallic parts that aren't very rust/corrosion resistant. If you want to immerse the pen further than it would be immersed in ink if you were filling it, it's probably going to need to be broken down into parts and dried before reassembly, else you'll be carrying around water stored in various places in the pen where there shouldn't be any. If you feel that you must clean the entire pen, and so must break it down, because of OCD or something, then do what you have to do, but don't do it unless your inner demons are forcing you to. I can't think of a rational reason to take things that far. Honestly, I think you'll be astonished at how well it works just to immerse the pen up to where it would be immersed in ink if you were filling it. With the pen filled first, the water inside the pen gets agitated by the ultrasonic, too. And unlike flushing alone, it's effective at removing ink deposits from nooks and crannies in the end of the section that only get there while you're filling it and then dry in place.
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