Here is a remedy from the RefWorks listserv when Write-n-Cite shuts down and improperly formats your paper.
“This is an issue with docx files. There are two solutions:
Save your docx file as a doc file, and re-run the Bib function.
If that doesn’t fix it, open Write N Cite (not RefWorks), and select “Revert to WNC v 2 document” from Tools. Give it a minute to revert and THEN
select “Convert to WNC III document.” Once it is converted, re-run the Bib function.
If that still doesn’t work, email your paper to RefWorks Tech Support with a description of your problem.”