Joining several stories in ID CS6 so that footnotes are numbered consecutively

I am working on a book in which much of the text has been typed directly into ID. These are separate stories and once they were input, the order in which they appear in the book has been changed, so, perhaps pages that contain the 5th story input, may have been moved to the front of the book. Consequently the text thread order is a little weird. My problem is that footnotes will start at 1 on each new story. Is there any way to automatically combine the text that retains its current order.

Thanks for any help.

Jon