Have you had a look at rsync? There is a DOS/windows version out there somewhere. It is very flexible once you get your head around it.
The other thing that occurs to me is that you might need to break this into two cycles of tasks/work. With subversion (and other) version control software you have a cycle of work:
i) update to get the latest version
ii) do stuff
iii) check in your new work
Translating that to your situation:
i) you sync from your PC to CF to get the latest copies on the CF
ii) you open the PDF on the iliad and scribble all over it
iii) you then sync from the CF back to the PC (before you download anymore that you want to sync to the iliad)
You say that your sync software won't do the third step. I'd be surprised if rsync won't. I can't try it now, maybe later.
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