I recommend that you work from the back of the document to avoid having the numbering mess you up.

If you have a set of endnotes in a new file, and superscripted numbers for them within your document, use the "Search: Up" option of Find to look for superscript from the end of the file. When you find a superscript that relates to one of your non-Word endnotes, delete it, then immediately insert a new endnote and paste the content. Word will insert a new endnote link and manage the sequencing. Then use the "find up" button on the vertical scroll bar to find the next instance to repeat.

I've done this fairly frequently for preparing manuscripts, and question whether it is practical to use VBA. A manual solution is quite quick, and allows you to deal with issues that would be hard to anticipate for a general VBA solution.