BK,
1. I would not suggest to apply the Windows fixes so far in advance of running the rebasing tool, at least not the client OS fix. That is becasue the newly created meetings (within that week) will also get moved by the rebasing tool even though they will look correct from the client side. If you have so much time between client OS fixes and rebasing tool, then client rebasing tool should be used and the users should choose not to modify the appointments created within that last week.
2. You should apply the OS patch 1st, then CDO patch and then run the rebasing tool. You should be able to do all of those rapidly one after the other.
MW, I think that #1 above adressed your question about if appointments created in the mean time will be broken or not? I have also fixed the URL to the KB, sorry about that!