Hi Nick,
Not sure if you've found a solution to this issue yet or not, but I was struggling with this same problem in CS6, (might be different in CS5.5) and finally realized, that the "LOG NOTE" field, isn't the right place to store your "log notes" for your clips. Instead, use the "Description" field. This field saves your notes for each clip when relinking, reloading and even replacing footage. One other thing I found useful in CS6, was that while you can edit the native files from your shoot, there also tends to be issues associated with doing this, like lag in scrubbing in the source monitor and varioius other lags through out the program, However, you can always convert your native footage to pro res or whatever, using Media Encder, then "Replacing" your footage in your bin with the new (So long as the file name remains the same) pro res files. Two cool things happen here, one: your "Description Field" where you log your notes about each clip stays intact, and your footage relinks not only in your bin, but in the timeline as well. Anyways, just thought I'd share that. I'm new to Premiere and I'm constantly discovering new cool things FCP 7 didnt offer me. Maybe you knew already. Hope this helps your issue or at least gives you some thoughts. Happy Editing.
Josh