Although the Enter RMA (SO-P-F) option has a "hide note" feature button, it does not appear to have the ability to hide individual line notes. You either have to print all notes or no notes. We specifically do not transfer RMA notes to Sales Orders, however, it also does not have the ability to transfer notes  
as "hidden" to Sales Orders (this being part of the reason why we do not transfer the notes).
 
It would be nice to be able to selectively hide and transfer notes by line item.
 
(from our Customer Service folks)
 
Val