Endnote formatted footnotes and transferring to design packages

This is probably off topic.

After years of getting footnotes right my typesetter did a sample and transferred my footnotes over and they lost all the formatting. I use Word. I kept saying how important it is and now she said she will follow my instructions!!!  I have public records, private papers and a full range of sources. I think she is going to copy my formatting manually and I have thousands fo footnotes. First I will have to recheck it all again and I don’t want to and I dont have the time. Secondly of course is the cost.( I have broken with tradition and each chapter starts with footnote 1. (Specific history so acceptable).

Has anyone else come aross this or does everyone self publish or create papers in a design package. 

Can anyone share experiences please?   Yes I discussed this at the interview but it wasn’t going to be a problem.