A bunch of my reference solutions are handwritten PDFs, and the writing is very pale. It doesn’t print well. The only way I’ve found to get the writing to print semi clearly is to set the printer to the highest quality settings, but when I do this, it takes upwards of an hour to print a 10 page document; this is undesirable, but the lower quality (with “toner saver” mode off) settings do not work. If I could just darken the pages I could print them.
As far as I know, Acrobat is treating your notes as embedded pictures, and as such, needs an external editor to change anything on them. What version of Acrobat are you using (Standard/Professional/Reader), and do you an image editing product installed on your computer (GIMP or Photoshop)?
I was using Foxit, but when I used Acrobat 8.0 Reader I noticed a 2x decrease in time-to-print. When I try the select tool, it only lets me select certain, random, parts of the page. I have a photo editor: “Microsoft Photo Editor”.
Reader doesn’t seem to want to let me copy all of the random bits. It will let me select a rectangle, but it will only copy part of that rectangle; ie all I can get out is a word or a number, when it has let me select a table.
This is the problem with using a Page Description Language (like postscript) as a document interchange format, and also a consequence of Print to PDF - you are at the mercy of the program used to generate the PDF. You see, Postscript describes what has to be done to get the desired image on the page - I have looked at the raw postscript for a kerned document, and each letter is placed on the page individually, and not necessarily in order. Selection in a PDF seems to involve attempting to grab all the text elements located within the selection range and then ordering them - which may not correspond to what you actually want, and probably will not give you what you need.
As for the handwritten notes, they will be bitmaps - maybe included as JPEGS, but possibly inserted as Postscript bitmaps into the datastream. Again, these may not be atomic images - whatever generated the PDF could have split the bitmaps into chunks for easier rendering.