Zotero — or any citation tool — needs to be able to update citations to ensure that they're accurate. If you fix some metadata in Zotero, or if you're using a style that requires given name disambiguation or ibid. or other things that depend on the context of the citations, or if you change the citation style, the citations will need to be updated to remain correct, and by modifying them yourself you're creating a situation where it can't do that while preserving your edits. So it has to ask you whether you want to leave the citation as permanently un-updated and possibly incorrect ("Yes") or revert your changes ("No").

(Also, you either left out a sentence from the dialog or are getting an earlier version of the dialog text because you're using Word 2008 and have an old version of the plugin. The current dialog text includes the line "Do you want to keep your modifications and prevent future updates?" The "Yes" and "No" buttons are admittedly confusing, but we're currently limited to those for technical reasons.)

If you make widespread changes to active citations and then try to use the plugin, you're going to get this message for every single citation that you updated.

Editing citations this way is almost always the incorrect approach, though, and it certainly makes no sense if you're later going to change styles. Data problems — capitalization, incorrect characters — should always be fixed in Zotero itself, not in the document, and you should customize citations using the prefix/suffix options and/or the Suppress Author option in the citation dialog for discursive citations. If you're unsure how to fix something properly without modifying the citation, let us know.

For certain rare scenarios, you can leave some notes in the text for things to fix, use Unlink Citations in a copy of the document right before submitting it, and then apply the manual corrections to the flat text.

If you want to fix the citations properly as I describe above, you can revert them by switching to a clearly different style and then looking for citations that haven't been updated. If you click in those and click Add/Edit Citation, it will prompt you to revert your changes.

Still don't understand implications of "Yes" or "No" choice. A citation that can't be updated?

I explained in detail above. "Updated" means updated by Zotero.

Can I delete it and replace it with a live citation?

Yes, but you can also just do what I said above to revert the changes.

"you can revert them by switching to a clearly different style and then looking for citations that haven't been updated." This is a problem. My memory is not so good I can recall maybe 100 sets of citations.

No, you're misunderstanding — I'm saying you can switch to a style that looks completely different, so that you can easily see which ones you've modified manually and told Zotero not to update.

I did not edit on the document within a citation set. Where I needed to change an item within a set, I used Edit Citation.

If you're getting this message, you somehow changed the citation text — that's what this is about. If you're using the classic citation dialog (as opposed to the default red bar), editing the citation in the dialog would be the same thing as editing it in the document. The point is that you shouldn't edit the citation text directly. You should either edit the metadata in Zotero or customize the citation as explained in the documentation I linked to above.

I was careful to capture margins of text on both sides of the citations when I moved them, to make sure I moved all the code with the citation set. Was this the right way to do it?

Yes. This is generally about editing the actual text of the citation, not about moving or deleting citations. If you did accidentally leave behind part of a citation while moving, that would be one way you'd get this, particularly if you see a blank entry or a single character for the "Modified" line, but that's just not very common in Word when using the default fields mode. (It's more common when using bookmarks, particularly in LibreOffice.)

Using Track Changes can also cause lots of problems with citations.

I think my error was planning to refresh the document all at once instead of after each delete or move.

No, there's no problem with that. Again, this really shouldn't happen with normal usage of Zotero unless you're making edits to the citation text.

" Yes, but you can also just do what I said above to revert the changes."

Then NO would be the better choice, as you can update the citation again (using the Edit Citation red bar or correcting the Zotero entry) before you get confused about what you're doing.

I was explaining how you can revert a citation that you had previously answered Yes for without needing to delete and reinsert it like you suggested. If you get the dialog and didn't mean to make changes, you should obviously answer No at that point to revert the changes.

If you get this error message and click either NO or YES, can you be assured the Zotero plug-in has updated all the other citations in the document? Or does it get stalled at an error?

First, just to clarify, it's not really an error message. It's a prompt for a decision Zotero can't make on its own.

It will appear as Zotero processes the citations in order, for every citation you modified since the last refresh. If you don't get some other error, everything should have updated correctly. If you force-quit Word, your document will be left in an undefined state.

(It seems there would be little use case for YES, you're buying yourself a bunch of additional document QA.)

Generally, you should answer No and change your workflow, but Yes is Yes because it's the option that doesn't delete your changes. People are going to make manual edits, even if they shouldn't, and it's not necessarily a problem to continue working in a document after saying Yes. The degree of resulting incorrectness depends on the style you're using and what other citations you add or delete in the document.

Now I'm really confused. Is using Edit Citation with the red bar the proper way to change a citation in a set?

What do you mean by "change a citation in a set"? You can certainly add or remove other citations in a multi-part citation by adding or removing the blue bubbles without triggering this dialog.

All this dialog means is that the text of the citation diverged from what it's supposed to be based on the underlying data. That can happen by typing in the document, editing the text in the classic citation dialog, accidentally deleting part of a citation, or having something go wrong with Track Changes. Generally people get this when they try to correct something in the citation (e.g., fix a misspelling, add a missing component, add a page number), and that's why I explained above the better ways of doing those things. If that's not what you did, then you can ignore that.

Modified: [since this is blank, is it necessary?]

It's not blank in general — it shows whatever's currently in the text of the citation, as I've explained above. If you're seeing it blank for every instance of this message, something very strange happened in your document, perhaps due to Track Changes or incorrect cutting/pasting. You can toggle Word field codes back and forth to find citations that are blank for some reason. Making sure Word is set to always use shading for fields rather than only shading them when they're selected can also help you make sure you haven't left parts of citations behind.

If you can reproduce getting this dialog in a new document for something that you don't think should trigger it, let us know, but it should work the way I describe above, and you should be able to see the expected behavior in a new document if you try to modify a citation's text by hand.

We'll see what we can do to clarify the dialog text.