The PAF info on notes says "There is no limit to the amount of notes that you can have." I was fairly sure that PAF 4 had a fairly generous limit, but PAF 5 doesn't have a limit.
I am with you where the extesive use of notes is concerned. Whenever I get a telephone call or email regarding anyone on my website, I look for them in PAF and in my PAF notes I immediately can find all my information on that person, with the full text of obits and other newspaper articles, biographies, local histories, every available census, interviews, contact info for other interested people (in confidential notes). PAF's notes IS my electronic filing cabinet. I have never lost any note yet.
What might have happened in your case?
If you export a gedcom file you can choose to exclude the notes. Then if this gedcom is imported into a new PAF file, the notes will be missing. When a whole family line has lost its notes, this seems like a possible answer, since this is how we tend to select people for export.
Notes can be lost during Match/Merge. When merging, you can choose whether or not to combine the notes for the two merged records. If you choose to not combine the notes, the notes for the deleted record will be lost.
Check your backups and other files with these particular family lines, starting with the most recent ones, to see if you can find a file that still has the notes. If you are successful, create a PAF file with a new name, and import the family lines that have the notes, and then do any necesary merging and linking. I like to keep merging to a bare minimum, so I like to plan it out on paper before-hand (who to export, import, merge, and link by marriage or birth).
PAF backup files use a ZIP format, but it just stores a copy of the PAF file as a compressed ZIP archive. It doesn't alter the contents of the file.
If you use PAF Insight, it creates its own backup each time you save a file. You can also access these backups looking for a file with the notes intact.
And you may have PAF 3 or PAF 4 files with the notes. Don't give up! Please!!!
Let us know how things go. If you need help pulling data from different files and combining them, let me know. I try to check this forum at least once a week.