I can't really tell what you are trying to do, but I think you need to know that when you make a cross-reference, FM inserts a Cross-Ref marker in front of the source, and you need to take care of that marker! Turn on the Text Symbols view so you can see it (and all other markers. Don't accidently delete it or else all cross-references to that source text will be broken.
If you want to cut, copy and paste Cross-Ref markers (or text containing Cross-Ref markers) then you have to be careful. The main restriction is that FM will not paste a Cross-Ref marker into a document if the document already has a Cross-Ref marker that is identical to the one you are trying to paste in. The logical conclusions of this are as follows:
If you want to paste in a sequence of identical paragraphs (with identical Cross-Ref markers) and then edit each marker in some systematic way, then sorry but you can't do it. The paragraphs will paste in alright, but without the Cross-Ref markers.
If you want to move a section that has a cross-reference marker at the front of it, make sure you do a CUT and paste. If you do a COPY and paste within the same document and then delete the original text, then you will have deleted the marker, and all cross-references to the moved section will now be unresolved - you'll have to either make new cross-references again or try to reconstruct the deleted Cross-Ref marker by hand (using the information found in a MIF version of the file that contains the unresolved cross-references).
Dave Hayes