Zotero's citation troubleshooting page makes a distinction that is easy to overlook: flat-text citations are not active citations, even when the punctuation on the page looks correct.
While drafting this recovery procedure, I used that distinction to separate appearance from function. It explains why "fix what looks wrong" is a poor starting point. Some of the most expensive damage is invisible.
A citation can still say (Nguyen, 2024) after its link to the reference manager is gone. A table of contents can show the right page number until a heading moves. A cross-reference can display Figure 2 while behaving like typed text. The returned DOCX may open, print, and look normal, yet no longer be a sound working document.
The clean copy should therefore be the recovery base. The humanized file supplies candidate wording. Reversing those roles means rebuilding live document parts inside the file least able to prove that they survived.
Before repairing anything, preserve three files with names that make their roles hard to confuse: clean-source.docx, damaged-return.docx, and recovery-working.docx. The working file should be a fresh copy of the clean source. Leave the other two untouched.
If the clean source seems to be missing, search old mail, team drives, copies held by collaborators, and backups before settling for a PDF. Microsoft Version History can open and restore earlier Office versions when the file uses OneDrive or SharePoint storage. That does not help a file that lived only on a local drive, but it is worth checking before rebuilding citations by hand.
A PDF is useful evidence for wording and page appearance. It cannot restore a live Zotero field, bookmark, section break, or table-of-contents relationship. Treat it as a reference, not as an editable source.
Next, compare the clean and returned DOCX files in Word. Microsoft's legal blackline instructions describe a comparison that shows changes in a third document while leaving both source files unchanged. Use the clean file as the original and the humanized file as the revision.
The comparison is a map, not the repair file.
When a number, quotation, method step, defined term, or claim boundary changed, the clean version and the underlying research record decide what is correct. When a citation or bibliography entry changed, the clean linked field and reference-manager library are the source of truth. When a heading, table, caption, footnote, page break, or section break changed, keep the clean object's structure.
Ordinary prose is the only part the damaged return should contribute. Even then, move it paragraph by paragraph. Keep wording only when its meaning matches the clean version and its citations still support the claim. Repair it when a useful sentence lost a qualifier or technical term. Discard it when the rewrite broadened a conclusion, changed a number, or made the sentence harder to defend.
This order feels slower than fixing the damaged file in place. It usually reduces uncertainty. Each decision becomes a small transfer of reviewed prose into known-good structure. You never have to wonder whether a repaired paragraph is sitting inside a still-broken citation field.
Zotero's Word plugin documentation says its Refresh command updates linked citations and the bibliography from the library. Its troubleshooting page also explains that manual citation edits can stop updates. So refresh is a functional test, not a cosmetic one. If the clean citation works and the returned one does not, keep or reinsert the linked citation from the clean side. Typing the brackets until they match only repairs the appearance.
Word fields need the same treatment. Put back each target heading, caption, or bookmark before testing anything that depends on it. Microsoft's Windows instructions give Ctrl+A and F9. A table can require its own selection and update. An error at that point means a dependency is broken. Do not type over the error message.
The repair is finished when every remaining difference from the clean source is intentional prose.
Compare the clean file with recovery-working.docx one more time. Use the reference manager's Refresh command on citations and its generated reference list. Update Word fields after their targets are final. Reopen the sources behind changed citation-bearing claims. Close the saved file, open it again, then make a PDF and inspect the pages containing tables, notes, section changes, and the reference list.
If any unexplained structural change remains, the file fails the recovery check. Keep working from the clean copy.
One more full-document humanizer run is tempting at this point, especially near a deadline. It also exposes every repaired object and approved paragraph to another set of changes. Work only on the passages that still need attention, and keep citations and structure outside that scope.
The rule I wrote at the top of the recovery notes became the whole method. Sound structure comes from the clean file. Proposed wording comes from the damaged one. Never ask the damaged file to prove that it repaired itself.
The complete recovery sequence is in this incident checklist.
