Adding notes to indexed folders

I have my reprint library, References, indexed, as it is large and I am constantly adding to it. It is arranged in folders labeled by topic. So I regularly synchronize. Two questions:

  1. Let’s say I rearrange the folders on my Powerbook (lumping two categories, and splitting another). When I use synchronize, do I create orphan folders on DtP? When do you choose to re-index References, vs Synchronize it?

  2. I am becoming a big fan of using DtP to take notes from books, emails, etc. Ideally, it would be great to add them to my indexed reprint folders according to topic (giving me a one stop shopping for all my different forms of media on, say, fractals). I am cautious tho, as I regularly synchronize these folders. Will that imperil any notes I’ve created within DtP and added to them?

Thanks for the help. DtP rocks.

Synchronizing adds, updates or removes folders/files if necessary and therefore this should work (without creating orphans).

Synchronizing does not remove any contents stored in the database of course and therefore this should work too.