whichever option I choose, Zotero proceeds to muck up all my footnotes so I barely know what has gone where.

Can you be more specific about what "muck up" means here? What exactly happens? Screenshots are welcome (you can upload to Dropbox, Imgur, etc. and link to them here)

Forgot to address this:

"You have modified this citation since zotero generated it. do you want to keep your modifications and prevent future updates? Clicking yes will prevent zotero from updating this citation if you add additional citations, switch styles, or modify the reference to which it refers. Clicking no will erase your changes."

What this means is that you inserted a footnote using Zotero and then manually edited it in Word by adding/deleting text to/from it (or at least that's what Zotero thinks). Now Zotero is trying to refresh the footnote, but if it does, your changes will be lost, so it's asking you if you want Zotero to keep your changes or re-generate the footnote.

Given above, you may be able to more easily re-trigger the error (in a copy of your document of course). I'm still not really sure what happens exactly and it would be quite difficult for us to figure it out without an ability to reproduce the problem reliably. So if you can come up with some steps that produce the issue and (if needed) a sample document, we can take a look.

Do you have "Track Changes" enabled?

you don't need to do this in classic view -- you can do it in quick format, too -- but you do need to do it in the word add-on, yes:
https://www.zotero.org/support/word_processor_plugin_usage#quick_format_citation_dialog

Hi everyone,

This is a great tool. I know this is a pretty old thread but I, too, am getting this error. For me I believe it happens when I restart things. First, my version of said "things" :

LibreOffice Writer 5.2.7.2
Zotero 5.0.74
OS: Linux (Debian 9).
Zotero Document Settings:
Citation Style -> Chicago Manual of Style 17th edition (author-date)
Language -> English (US)
Store Citations as -> Reference Marks
Automatically update citations (checked)

This morning I started up my document, then started up Zotero. When adding a reference I got the above-mentioned error. It iterates over every citation in my document, showing this message for each one. When it shows the Original and the Modified version of the citation, the Original never has page numbers. So I wonder if some setting is being forgotten when the document is closed, so that it thinks every reference having page numbers has JUST been modified.

The quick and dirty fix for this is to just keep clicking "YES" to keep my changes. But as my document grows, this gets tedious. Happy to help trouble-shoot in any way. Is there an "enable debugging" option that can log more output on what Zotero is doing at this stage?