While I think that you should go back and "hg mv" the files, I'll note that webrev doesn't do the right thing here -- it will see the file as being added and then removed, rather than moved. I've got a wad for that, if you want me to dig it up, but otherwise, you're going to have to hand-roll those parts of the webrev. David Comay's been doing this for us in the pkg5 gate for a while, so he can give you details if you can't figure it out.
As for how to go back and record the move, my guess is that the simplest way is to add the file as it existed previously into a new changeset, then recommit. That should make it look like the file wasn't touched. Then set aside the destination file, hg mv the source to the destination, and copy the correct new contents on top, then commit. Obviously try that out in a throwaway workspace first. :) Danek