Is this a single document, or a Book (.indb) that holds multiple files?
Sometimes documents can pick up weird behaviour after being repeatedly saved.
When these hiccups start happening you could try File>Save As>IDML
Open the IDML and it opens as "Untitled"
As soon as it opens try the print to pdf option.
For the record - Printing to PDF isn't very good practice. And usually printing companies perform impositions themselves - they prefer to get the file as page 1 - end in consectuive order, 1,2,3,4,etc.
A Book that contains multiple files.
Great idea, only this is a Book and the only save option I have (that I know of!) is "Save Book" in the Book Panel (where I can manage all the files in the Book).
Try saving each of the individual files as .idml, then reopen and save as new .indd files (don't overwrite the old ones) that you can add to a new .indb Book file.