Footnote enigma

So, I have a long document with about 900 endnotes. I later added some more material that had footnotes and told the program (InDesign) transform them into endnotes. It did, but started a whole new set of Endnotes with new numbering. Once I realized what had happened, a week or so later, I have tried to work out what happened and a way to fix it. 

• I checked to see if I somehow had told the program to start numbering all over again - and so far have not found anything.
• I tried erasing each endnote reference and then putting in a new endnote. Same problem.
• No matter what I try, same thing happens. I have had to resort to copying each individual endnote then going to the reference number in the copy, erasing the endnote reference and putting in a footnote and pasting the copy into the footnote. 
• This is working, in the sense that I now have footnotes with the copy, but it is weird when the rest of the whole document is endnotes.

Does anybody have any idea what I can do. I could try converting all my endnotes to footnotes, then switching them back to endnotes. But I am afraid I will screw up all of my formatting in the document. Again, we are talking 550 pages 8x11 so I don't want to have to go back and reformat.

Thanks again for your help,

Dan