Yes, non-Western characters are sometimes encoded strangely in the cleaned files, but XTG, like .qsc, is a tagged format that is imported into Quark Xpress. That is to say, it's an interim file, not an end-formatted document.
Just because the XTG looks strange the Quark Xpress document doesn't necessarily have to exhibit the same problems, at least not if the proper Greek fonts are assigned to the affected text frames.
So, why don't you just let your client try if this file is usable and let us know if the problem persists?
after the client inserted the translation into Quark Express, the characters were shown correctly again.
Thank you very much for the help!