I am only speculating, I never saw a copy of PAF before version 4, and it isn't my main genealogy program.
What I think you, and the help files, are talking about, is that in earlier versions of PAF, before 3, the sources were typed into the notes field as there wasn't yet a dedicated source field.The notes were stored in an INDIV2.DAT file. If you don't have that file left over from a n early PAF program, there is no use in looking for it. Those instructions sound to me to be for converting Version 2.31 files to version 3 or 4. Once they are converted to 3 or 4 that way, then they should convert to 5.
If you have things in notes that should be in the sources, it sounds to me like you are going to have to cut and paste the information from notes to sources for each individual. It isn't hard to do, just time consuming.
I highlight the text I want to move by moving the mouse cursor to the front of it, pressing the regular button and drag the highlight to the end of the text before Irelease the button. Once it is highlighted, I press [ CTRL ]-[ C ] to copy that text. Then move the cursor to the position you want the text, click once in the position so you know the cursor is there, then press [ CTRL ] - [ V ] to paste it there.When you get it right, you can go back and highlight the original text, in the note and press the [ Delete ] button to erase it.After you have done it a few times you can CUT rather than copy the text from the notes by pressing [ CTRL ]-[ X ] instead of Ctrl-C, that way you don't have to go back and erase.
I have heard others talk about renumbering/reordering sources, quite frankly, I know little about sources, but I always thought sources were numbered by the report, the first one that is refrenced is #1, the next one is #2 etc.If they were permanently numbered by the program, and you generated a different report, with different individuals, wouldnt the numbering be way off?So, it shows, I don't know anything about this subject.