there is something that I cannot understand. What method did you follow to transfer your course from the old server to the new one?
Did you make a full backup (database, moodledata and moodle) and then install it in a new server?
Did you perform a course backup and restore in the new (just installed) site?
About glossaries, are you saying that concepts hi-lighted in your new server are pointing to the old server? Or are you saying that entries in your new server have their attachments pointing to the old server?
Can I see that in action?
The example XML file you've sent is really a simple one. It hasn't attachements or anything else. If I import it in my test server I see the entry without problems at all.
Definitively, I cannot understand the problem and it's bad news to try to solve it.
Waiting for more info, ciao