Before you can use the Separation Repair tool, you must insert all separations into one PDF document (if they're not already in one document). You need to do this if each of the refined PDF pages for a job contains only one separation.
If one refined PDF page contains all separations for the job, but separations are incorrectly grouped, you don't need to insert the separations into one PDF document. You can use the Separation Repair tool.

1. In Acrobat, open the PDF page that contains the cyan separation.
2. Select Document > Insert Pages.
   
   
   
   
3. In the Select File to Insert dialog box, locate the PDF that contains the magenta separation.
4. Select the file, and click Open.
   The Insert dialog box appears.
   
   
   
   
5. In the Location box, select After.
6. In the Page area, click Last page.
7. Click OK.
8. Repeat the above steps for each separation until all separations for the job are in one PDF document.

When you finish, you can use the Separation Repair tool.