The annotate function limits you to about 2K per note.
Notes are stored in your C:\WINDOWS (or wherever you installed WIN.COM) in a file named IPWIN.ANN. Making that file readonly won't work to prevent change to your notes--Windows won't open WINHELP's annotate function.
Remember you can annotate any topic in the database...and you can build annotations via the clipboard.
Finally, the annotate window is modal--that is, it won't let you return to the active help file until you close it.