Here is what I would do -
1) Bring all data upto date on the old USB drive - so that it is backed up all nicely on one location.
2) Plug in your new USB disk
3) Do a normal upgrade to SyncToy 2.0
4) If your new USB disk got the old drive letter, we will pop a message saying it does not appear that the two folders in each folder pair have synchronized and if can continue by creating metadata on the new folder. However - be sure to create the top level folder on the new disk ( as you rightly point out above).
5) If on the other hand your USB disk gets the old drive letter, you have no other option that to delete the old folder pairs and recreate them.
Thanks
Deepa