Deleted one footnote, moved a few around, and now they're all numbered wrong
I deleted the first footnote in a paper, and now the first footnote is numbered 2, and I moved some things around so not all my numbers are crazy. Tried refreshing citations, only made it worse.
As adamsmith says, Zotero itself is not the source of the problem on this occasion. Word controls the footnotes, so those are Word's numbers. Zotero is trusting the data that comes out of Word so things have gone a little zany, but once the Word blip is sorted out, it should come right for you.
Keep a backup copy of the document handy, though, just in case.