This is my problem:
This has nothing to do with this here, at least not from my side. At least in this case I would not mind if CT forgets the state of unchecked segments. I can work with these segments without any problem, but I cannot remove them in one go.
The "Remove target segments" feature is designed to work with CafeTran project files. It may or may not work for unknown xliff files created in other translation tools. You can submit a ticket with the attached sample mqxliff file.