Keeping notes out of the pack
Your client's comments never enter a PDF. Not one of them, on any export, with no switch to change it. The thread lives where it was left.
Your own note fields are a different question, and the answer depends on which export you are making.
The shoot pack
Frames, shot data and descriptions, plus the client note on a frame if you wrote one. That field exists precisely so there is somewhere to put a line the crew should read, and it is off by default: turn on Client notes in the export options to include it.
Your director's and production notes are not on the shoot pack.
The shot list
The internal shot list is the document that carries them. Its PDF and CSV both have a Director notes and a Production notes column, because that list is for your side of the job and never leaves it: a share link carries the board, not the shot list.
Where the conversation lives
On the client's own review page, where they left it, and on your board beside the frame it belongs to. If you need a written record of the conversation, take it from the board rather than from the pack.