Is the XML fragment a file entity created by Arbortext Editor, or another fragment type?
If you open the fragment in Arbortext Editor and use from the Command: line
edit -current -untagged
and then
1) Remove the fragment comment
2) Save the document
Does this meet your need?
If so, then it should not be too hard to script this in Java, Javascript or ACL.
Anyone have a suggestion for this issue?