I have used unlinking a marriage and then exporting (I think I selected the one marriage partner and used "All Related" in the Relationship filter) to create gedcom files of the separate lines. Then I created new PAF data files with new names and imported the respective gedcom files. This allowed me to easily filter out confidential data before sharing the files with relatives (which was my purpose in splitting the file).
Your purpose for splitting the file is a little different, so you would not filter out any information. But the same basic process should work.
Let me know if you have been able to backup to other locations since changing the Tools > Preferences > Folders for the backup location.