Was your document stored in any cloud storage service? Also, could you confirm whether you were able to change your in-text citations to temporary ones (a.k.a. “unformatting” where the in-text citation now has curly braces and displays the author name and record number). If you are able to change the in-text citations to temporary citations then change them back into formatted citations then at least we know the Endnote field codes are still present in the document.
Also, when you changed the in-text citations to temporary citations, did you proceed to check for any corrupt citation as described in that knowledge base article? If you are unable to locate the corrupt citation, suggest you try deleting the first citation and see if the remaining citations update to a correct sequence of numbers. If so then it seems that the first citation was the problem so just reinsert the citation and see if the number sequence updates correctly