I think you need to step back and consider whether your current filing system is scalable for the long, long years to come.
My belief is that the use of computers leads us into all sorts of lazy habits and filing is probably the worst of these. Set up a standard filing system which will work irrespective of machine or o/s and then you will not need to concern yourself when the indexing system changes/freezes/locks out or whatever.
Better still keep all your files on a central repository and access them from there – in the new connected world I challenge you to reduce your “IP-footprint” in terms of data storage.

I don’t know if anyone else suggested this yet, but why not use NTFS’s version of soft/hard linking to duplicate both structures without moving anything? http://alax.info/blog/ntfslinks is the one I use when I’m on windows; it’s free, or you can do it without any utilities from the command line.

When I was using Vista, I was able to get at my documents folder from \Documents and Settings\myname\My Documents, \Users\myname\Documents, and \home\myname\documents (as someone who uses Linux the most, the last was the one I used most of the time.) It can confuse some scanning programs, but it makes syncing between different OSes easy — and some poorly-programmed older Windows machines work more nicely with that kind of setup anyway.

James I’m a bit confused. If you embed links in OneNote using the P1610 on XP, then those links wouldn’t work on the 2710p since it’s on Vista’s file structure right? Or does OneNote automatically redirect to the correct path in Vista? I guess what I’m trying to say is that if you don’t build the structure on the Fuji to match Vista’s, you would have a conflict with any links you create in Vista or when you try to open those links on the HP that were created on the Fuji. Wouldn’t you?