I have a 641 page PDF created in Adobe Acrobat 9. When used with Reader, sometimes the file can not be saved. Message I get is "The document could not be saved. The file may be read-only, or another user may have it open. Please save the document with another file name or in a different folder."
Do you have Reader on the same computer as Acrobat? If so this is not supported in Acrobat 9. If you have worked with the file in Acrobat 9, the application and OS may have not released its hold on the file. You will need to change the name when saving.