Word does as it's told, so at some point it's been told something peculiar. 1,000 notes shouldn't be a problem in itself.
I would divide the document into sections so the endnotes fall at the end of each section rather than at the end of the document. You'll have to tell Word that's where you want them to be. (You can revert them to the end of the document once you've sorted it.)
There's a good chance that your problem only appears in certain sections. Once you've identified where it is, you can start working out what it is. And if you do have to replace endnotes, you can minimise the number this way.
You mention 1,000 footnotes. In addition to the endnotes? Is that a separate issue? Or did you mistype?
Edited to add: Are the problems at both ends? Are you both working with the same version of Word? Neither of you doing something creative like moving a doc or docx file from something like Open Office or Office Libre to Word? This sort of thing can happen with 'compatible' software.
An alternative is that the error was inserted due to some copy/pasting that added a command from another file. In which case you might need to sternly tell your client to paste in unformatted text (paste from menu using A rather than Ctrl+ V).
