That's what I was thinking, but I can't seem to delete pages from the PDF. A have it set to "No Security" and I can copy and paste, I just can't cut (other than single lines of text via the "touch up" tool). I'll go through the help and what not again...
This is with Adobe Acrobat Professional 6.0,
EDIT: Ok, it looks like I found the solution - you can delete pages by deleting their thumbnail image; and the bookmarks seem to remain. Thanks for the help!