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Qelix: I guess, being "Chained" is seen as a sign(?) of slavery, be it slaves of any form.
As for why that Elf Girl was treated as a Criminal Slave and locked up like that, well i guess the only possible reason would be that she was caught committing an assassination. Even though she was forced to do them by her previous owner, she still committed a crime. So while she had been pardoned from execution for her crimes, she is still someone who had assassinated other people, so they currently kept her locked up.
As for the "Not to harm another human being"-clause, i think it only applied while a Slave Contract is active (not while she was locked up in her cell in that Slave Seller Shop).
Also the "Not to harm another human being"-clause was applied on her because of her assassination skills which the Kingdom probably believe to be really high. So, while they couldn't execute her because of some slavery related laws, they couldn't let her be completely free either, because it was easily possible that some other people might immediately take her as slave, and have her assassinate various people. So, the best way to make a Assassin Slave useless is to apply that clause (though the question remains whether the term "human being" also include other Race people like BeastFolk, Dark Elf, etc or not).