I have been working with support since August 2008 on this issue
(support case 113877).
The responses have not been very good, but after totally turning off
syncing, removing the BBEdit folder on my iDisk and turning on one
machine, leaving it for a week or so and then turning on the other, it
has synced almost all stuff. One or two files did not sync to the new
machine. Fies I then tried to get to sync back have not worked.
I am less than impressed with the syncing and, in this case only, with
BBEdits support.
I will manually copy the stuff from now on.
My advise, give up and do it manually.
Doug