A family of Microsoft word processing software products for creating web, email, and print documents.
In my experience, converted documents from any other program will always be problematic for editing. The conversion introduces formatting practices that are not native to Word with workarounds by the conversion process.
At this stage, fixing it is going to be a major project, I hope you have an assistant.
My recommendation would be to create a new Word document and paste the content from your existing one as plain text. This is going to mess up your endnote connections.
Then edit that document, doing your formatting using Styles, and re-add the endnotes, as Word endnotes. Make changes to how these look by modifying the Endnote text and Endnote reference styles.
This is a lot of work. You will also have to add any figures/illustrations back and caption them.
Do not allow any editing in the online or mobile versions of Word.