You are required to log any transaction made of a C&R firearm while your 03 FFL is in effect. Feel free to not log them if you wish- it's your license and your decision. I don't understand why logging a transaction is so difficult, so my practice is to log any C&R acquired or disposed, with or without the license (items acquired before the license are not logged unless they are disposed). To me, it is almost no work for the upside of not worrying at all about consequences. If they ever audit (unlikely, but not impossible), the worst they will do is say "don't log this." If they find unlogged transactions that should be, I would be concerned about license suspension or whatever they dream up. No downside to doing it, lots of upside. For me, a no-brainer, but I am not into living dangerously.
Unlike an 01 FFL, everything you get is owned personally by you, and is part of your "collection." This to me indicates that
I have read question/answers from the ATF (I looked for it, and I can't remember where I found it), and their interpretation is the same as my practice. At the end of the day though, it's your choice as to what you do.
I sent an email to the national licensing center for clarification. I'll let you all know how it goes (I'll start a new thread under "general" for it).