First, if it isn't inside the bleed it won't be in the PDF unless you include slug and it's inside that.
Second, could the object itself be locked? The default preference from CS5 forward is to not allow selection of locked objects (first thing I change).
Is it included when you do a Select All?
Oh, duh! Yes, it was locked. I unlocked the spread and it selected right away. Many thanks!
Now, about that Notes tool......
Click inside a text frame where you want to leave a note.
I never use it, myself -- leaving notes for yourself is almost as bad as talking to yourself, and if I really need to remember something I add it as a non-pinting object in bright red.
"A non-printing object in bright red."
Would you give an example, please? In particular, I have a magazine column and beg the editor NOT to change "its" to "it's" and stuff like that. Can I write to him with "ink" that won't print? Do tell!
And thank you for your help today!
Two ways to do it...
Add a layer and set the layer properties to non-printing, put your notes there, OR, make a text frame anywhere, open the Attributes panel, and select the Non-Printing checkbox.
This isn't a note, but it is a non-printing frame that was used to put the (modified) title of the chart below (an Illusrtator file) into the TOC. If you squint you can see that the linvisibles layer name is in Italics because the layer is non-printing. I've put the attributes panel in the shot, too so you can see where you would check non-printing if the frame needed to be on a printable layer.
Sadly, nobody noticed the typo and it made it into print on the first edition.