I have a large document (first part of my thesis) that has about 50
references in IEEE style in it. I made them by creating a list with numbers
in square brackets at the end of the document, then cross-referencing those
paragraph numbers in the text, where each "paragraph" is the bibliographic
reference. Then, if I needed to insert a new reference between two
references, I just inserted a list item where necessary (in IEEE referencing,
the Bibliography shows references in the order in which they appear in the
text), and updated the fields so that the in-text cross-references were
correct.

At some point along the way, the cross-reference fields have messed up, and
now if I try to update them, the fields change from the number in square
brackets (paragraph number) to the page number where the reference is.

Is this a known bug? Is there any way I can automatically reconnect the
in-text cross-references to the appropriate paragraph number?