I have Acrobat X Pro.
I have used it to merge pdf documents (chapters) into a single pdf (book) .
I'd like to save the list of individual pdf files and their order so that if I make a change to one of the pdfs it is easy to generate another version of the book.
I don't believe this is possible with Acrobat.
Were the files created in InDesign by chance? If so, you should try creating an .indb (InDesign Book) file. This allows you to have individual files for each chapter, but it allows you to export the whole book easily to pdf when you are finished, or have made edits to an individual chapter.
here a link to an old vbScript, which should do what you want, merging files based on a simple file list file.